AMBER Archive (2003)

Subject: Re: Does Leap has a problem with Isoleucines?

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• In reply to: Frederico.Miranda_at_ibmb.uib.no: "Does Leap has a problem with Isoleucines?"
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Dear Frederico,

I think, the problem is not so much because of leap but because of the
atom names in your pdb file. Leap finds atoms with the names CG, CD2,
OG, and NZ for the residue ILE and can't map them to what it expects for
ILE from its library files (see e.g.
$AMBERHOME/dat/leap/lib/all_amino94.lib). Something must have gone wrong
in one of your earlier steps. Check where e.g. residue 8 becomes ILE
while it is ASP in the original pdb file. If this doesn't help, we need
more detailed information about the single steps you performed up until
this point.

Best regards

Holger

Frederico.Miranda_at_ibmb.uib.no wrote:
>
> Hello, I've done the tutorial for plastocyanin, and after protonating the
> protein, and putting the file in leap, with leaprc.ff94 I end up getting this:
>
> FATAL: Atom .R<ILE 8>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 28>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 30>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 30>.A<CD2 21> does not have a type.
> FATAL: Atom .R<ILE 32>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 34>.A<CD2 20> does not have a type.
> FATAL: Atom .R<ILE 34>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 42>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 44>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 44>.A<CD2 21> does not have a type.
> FATAL: Atom .R<ILE 46>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 48>.A<CD2 20> does not have a type.
> FATAL: Atom .R<ILE 48>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 70>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 78>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 92>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 94>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 102>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 104>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 104>.A<CD2 21> does not have a type.
> FATAL: Atom .R<ILE 106>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 108>.A<CD2 20> does not have a type.
> FATAL: Atom .R<ILE 108>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 124>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 126>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 126>.A<CE1 21> does not have a type.
> FATAL: Atom .R<ILE 128>.A<CD2 20> does not have a type.
> FATAL: Atom .R<ILE 128>.A<CE2 21> does not have a type.
> FATAL: Atom .R<ILE 128>.A<CG 22> does not have a type.
> FATAL: Atom .R<ILE 130>.A<CE1 20> does not have a type.
> FATAL: Atom .R<ILE 130>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 132>.A<CE2 20> does not have a type.
> FATAL: Atom .R<ILE 132>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 132>.A<CD2 22> does not have a type.
> FATAL: Atom .R<ILE 134>.A<CZ 20> does not have a type.
> FATAL: Atom .R<ILE 134>.A<CE1 21> does not have a type.
> FATAL: Atom .R<ILE 134>.A<CE2 22> does not have a type.
> FATAL: Atom .R<ILE 151>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 153>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 153>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 155>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 155>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 163>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 165>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 173>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 175>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 175>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 183>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 185>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 185>.A<CE1 21> does not have a type.
> FATAL: Atom .R<ILE 187>.A<CD2 20> does not have a type.
> FATAL: Atom .R<ILE 187>.A<CE2 21> does not have a type.
> FATAL: Atom .R<ILE 187>.A<CG 22> does not have a type.
> FATAL: Atom .R<ILE 189>.A<CE1 20> does not have a type.
> FATAL: Atom .R<ILE 189>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 191>.A<CE2 20> does not have a type.
> FATAL: Atom .R<ILE 191>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 191>.A<CD2 22> does not have a type.
> FATAL: Atom .R<ILE 193>.A<CZ 20> does not have a type.
> FATAL: Atom .R<ILE 193>.A<CE1 21> does not have a type.
> FATAL: Atom .R<ILE 193>.A<CE2 22> does not have a type.
> FATAL: Atom .R<ILE 201>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 203>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 214>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 216>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 221>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 223>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 223>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 225>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 225>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 239>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 241>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 241>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 249>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 251>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 251>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 253>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 253>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 253>.A<CE 22> does not have a type.
> FATAL: Atom .R<ILE 255>.A<CE 20> does not have a type.
> FATAL: Atom .R<ILE 255>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 255>.A<NZ 22> does not have a type.
> FATAL: Atom .R<ILE 257>.A<NZ 20> does not have a type.
> FATAL: Atom .R<ILE 257>.A<CE 21> does not have a type.
> FATAL: Atom .R<ILE 257>.A<CD 22> does not have a type.
> FATAL: Atom .R<ILE 280>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 282>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 282>.A<CE1 21> does not have a type.
> FATAL: Atom .R<ILE 284>.A<CD2 20> does not have a type.
> FATAL: Atom .R<ILE 284>.A<CE2 21> does not have a type.
> FATAL: Atom .R<ILE 284>.A<CG 22> does not have a type.
> FATAL: Atom .R<ILE 286>.A<CE1 20> does not have a type.
> FATAL: Atom .R<ILE 286>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 288>.A<CE2 20> does not have a type.
> FATAL: Atom .R<ILE 288>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 288>.A<CD2 22> does not have a type.
> FATAL: Atom .R<ILE 290>.A<CZ 20> does not have a type.
> FATAL: Atom .R<ILE 290>.A<CE1 21> does not have a type.
> FATAL: Atom .R<ILE 290>.A<CE2 22> does not have a type.
> FATAL: Atom .R<ILE 298>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 300>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 300>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 302>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 302>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 302>.A<CE 22> does not have a type.
> FATAL: Atom .R<ILE 304>.A<CE 20> does not have a type.
> FATAL: Atom .R<ILE 304>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 304>.A<NZ 22> does not have a type.
> FATAL: Atom .R<ILE 306>.A<NZ 20> does not have a type.
> FATAL: Atom .R<ILE 306>.A<CE 21> does not have a type.
> FATAL: Atom .R<ILE 306>.A<CD 22> does not have a type.
> FATAL: Atom .R<ILE 314>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 316>.A<ND2 20> does not have a type.
> FATAL: Atom .R<ILE 316>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 316>.A<OD1 22> does not have a type.
> FATAL: Atom .R<ILE 324>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 326>.A<ND2 20> does not have a type.
> FATAL: Atom .R<ILE 326>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 326>.A<OD1 22> does not have a type.
> FATAL: Atom .R<ILE 348>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 350>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 350>.A<CE1 21> does not have a type.
> FATAL: Atom .R<ILE 352>.A<CD2 20> does not have a type.
> FATAL: Atom .R<ILE 352>.A<CE2 21> does not have a type.
> FATAL: Atom .R<ILE 352>.A<CG 22> does not have a type.
> FATAL: Atom .R<ILE 354>.A<CE1 20> does not have a type.
> FATAL: Atom .R<ILE 354>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 356>.A<CE2 20> does not have a type.
> FATAL: Atom .R<ILE 356>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 356>.A<CD2 22> does not have a type.
> FATAL: Atom .R<ILE 358>.A<CZ 20> does not have a type.
> FATAL: Atom .R<ILE 358>.A<CE1 21> does not have a type.
> FATAL: Atom .R<ILE 358>.A<CE2 22> does not have a type.
> FATAL: Atom .R<ILE 363>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 365>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 365>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 367>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 367>.A<CG 21> does not have a type.
> FATAL: Atom .R<HIC 369>.A<N 1> does not have a type.
> FATAL: Atom .R<HIC 372>.A<H 1> does not have a type.
> FATAL: Atom .R<HIC 372>.A<CA 2> does not have a type.
> FATAL: Atom .R<HIC 374>.A<HA 1> does not have a type.
> FATAL: Atom .R<HIC 374>.A<C 2> does not have a type.
> FATAL: Atom .R<HIC 374>.A<O 3> does not have a type.
> FATAL: Atom .R<HIC 374>.A<CB 4> does not have a type.
> FATAL: Atom .R<ILE 375>.A<CG 20> does not have a type.
> FATAL: Atom .R<HIC 376>.A<HB3 1> does not have a type.
> FATAL: Atom .R<HIC 376>.A<HB2 2> does not have a type.
> FATAL: Atom .R<HIC 376>.A<CG 3> does not have a type.
> FATAL: Atom .R<HIC 376>.A<ND1 4> does not have a type.
> FATAL: Atom .R<HIC 376>.A<CD2 5> does not have a type.
> FATAL: Atom .R<ILE 377>.A<CD2 20> does not have a type.
> FATAL: Atom .R<ILE 377>.A<NE2 21> does not have a type.
> FATAL: Atom .R<ILE 377>.A<CG 22> does not have a type.
> FATAL: Atom .R<HIC 378>.A<HD2 1> does not have a type.
> FATAL: Atom .R<HIC 378>.A<CE1 2> does not have a type.
> FATAL: Atom .R<ILE 379>.A<CE1 20> does not have a type.
> FATAL: Atom .R<ILE 379>.A<ND1 21> does not have a type.
> FATAL: Atom .R<ILE 379>.A<NE2 22> does not have a type.
> FATAL: Atom .R<HIC 380>.A<HE1 1> does not have a type.
> FATAL: Atom .R<HIC 380>.A<NE2 2> does not have a type.
> FATAL: Atom .R<ILE 381>.A<NE2 20> does not have a type.
> FATAL: Atom .R<ILE 381>.A<CE1 21> does not have a type.
> FATAL: Atom .R<ILE 381>.A<CD2 22> does not have a type.
> FATAL: Atom .R<HIC 382>.A<HE2 1> does not have a type.
> FATAL: Atom .R<HIC 382>.A<CU 2> does not have a type.
> FATAL: Atom .R<ILE 389>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 391>.A<ND2 20> does not have a type.
> FATAL: Atom .R<ILE 391>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 391>.A<OD1 22> does not have a type.
> FATAL: Atom .R<ILE 414>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 416>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 416>.A<CE1 21> does not have a type.
> FATAL: Atom .R<ILE 418>.A<CD2 20> does not have a type.
> FATAL: Atom .R<ILE 418>.A<CE2 21> does not have a type.
> FATAL: Atom .R<ILE 418>.A<CG 22> does not have a type.
> FATAL: Atom .R<ILE 420>.A<CE1 20> does not have a type.
> FATAL: Atom .R<ILE 420>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 422>.A<CE2 20> does not have a type.
> FATAL: Atom .R<ILE 422>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 422>.A<CD2 22> does not have a type.
> FATAL: Atom .R<ILE 424>.A<CZ 20> does not have a type.
> FATAL: Atom .R<ILE 424>.A<CE1 21> does not have a type.
> FATAL: Atom .R<ILE 424>.A<CE2 22> does not have a type.
> FATAL: Atom .R<ILE 432>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 440>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 442>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 442>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 450>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 458>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 460>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 468>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 470>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 470>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 472>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 472>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 480>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 482>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 508>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 524>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 526>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 534>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 536>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 536>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 538>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 538>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 538>.A<CE 22> does not have a type.
> FATAL: Atom .R<ILE 540>.A<CE 20> does not have a type.
> FATAL: Atom .R<ILE 540>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 540>.A<NZ 22> does not have a type.
> FATAL: Atom .R<ILE 542>.A<NZ 20> does not have a type.
> FATAL: Atom .R<ILE 542>.A<CE 21> does not have a type.
> FATAL: Atom .R<ILE 542>.A<CD 22> does not have a type.
> FATAL: Atom .R<ILE 553>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 555>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 563>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 565>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 565>.A<SD 21> does not have a type.
> FATAL: Atom .R<ILE 567>.A<CE 20> does not have a type.
> FATAL: Atom .R<ILE 567>.A<SD 21> does not have a type.
> FATAL: Atom .R<ILE 567>.A<CG 22> does not have a type.
> FATAL: Atom .R<ILE 575>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 577>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 585>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 587>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 587>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 595>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 597>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 597>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 605>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 613>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 615>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 615>.A<CD2 21> does not have a type.
> FATAL: Atom .R<ILE 617>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 619>.A<CD2 20> does not have a type.
> FATAL: Atom .R<ILE 619>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 627>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 629>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 629>.A<CD2 21> does not have a type.
> FATAL: Atom .R<ILE 631>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 633>.A<CD2 20> does not have a type.
> FATAL: Atom .R<ILE 633>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 641>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 643>.A<ND2 20> does not have a type.
> FATAL: Atom .R<ILE 643>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 643>.A<OD1 22> does not have a type.
> FATAL: Atom .R<ILE 659>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 661>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 661>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 663>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 663>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 663>.A<CE 22> does not have a type.
> FATAL: Atom .R<ILE 665>.A<CE 20> does not have a type.
> FATAL: Atom .R<ILE 665>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 665>.A<NZ 22> does not have a type.
> FATAL: Atom .R<ILE 667>.A<NZ 20> does not have a type.
> FATAL: Atom .R<ILE 667>.A<CE 21> does not have a type.
> FATAL: Atom .R<ILE 667>.A<CD 22> does not have a type.
> FATAL: Atom .R<ILE 681>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 683>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 683>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 691>.A<OG1 20> does not have a type.
> FATAL: Atom .R<ILE 693>.A<OG1 20> does not have a type.
> FATAL: Atom .R<ILE 703>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 705>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 705>.A<CE1 21> does not have a type.
> FATAL: Atom .R<ILE 707>.A<CD2 20> does not have a type.
> FATAL: Atom .R<ILE 707>.A<CE2 21> does not have a type.
> FATAL: Atom .R<ILE 707>.A<CG 22> does not have a type.
> FATAL: Atom .R<ILE 709>.A<CE1 20> does not have a type.
> FATAL: Atom .R<ILE 709>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 711>.A<CE2 20> does not have a type.
> FATAL: Atom .R<ILE 711>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 711>.A<CD2 22> does not have a type.
> FATAL: Atom .R<ILE 713>.A<CZ 20> does not have a type.
> FATAL: Atom .R<ILE 713>.A<CE1 21> does not have a type.
> FATAL: Atom .R<ILE 713>.A<CE2 22> does not have a type.
> FATAL: Atom .R<ILE 721>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 723>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 723>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 751>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 753>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 753>.A<CD2 21> does not have a type.
> FATAL: Atom .R<ILE 755>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 757>.A<CD2 20> does not have a type.
> FATAL: Atom .R<ILE 757>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 765>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 767>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 775>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 777>.A<ND2 20> does not have a type.
> FATAL: Atom .R<ILE 777>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 777>.A<OD1 22> does not have a type.
> FATAL: Atom .R<ILE 785>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 787>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 787>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 789>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 789>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 789>.A<CE 22> does not have a type.
> FATAL: Atom .R<ILE 791>.A<CE 20> does not have a type.
> FATAL: Atom .R<ILE 791>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 791>.A<NZ 22> does not have a type.
> FATAL: Atom .R<ILE 793>.A<NZ 20> does not have a type.
> FATAL: Atom .R<ILE 793>.A<CE 21> does not have a type.
> FATAL: Atom .R<ILE 793>.A<CD 22> does not have a type.
> FATAL: Atom .R<ILE 807>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 809>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 809>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 817>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 819>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 819>.A<CE1 21> does not have a type.
> FATAL: Atom .R<ILE 821>.A<CD2 20> does not have a type.
> FATAL: Atom .R<ILE 821>.A<CE2 21> does not have a type.
> FATAL: Atom .R<ILE 821>.A<CG 22> does not have a type.
> FATAL: Atom .R<ILE 823>.A<CE1 20> does not have a type.
> FATAL: Atom .R<ILE 823>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 825>.A<CE2 20> does not have a type.
> FATAL: Atom .R<ILE 825>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 825>.A<CD2 22> does not have a type.
> FATAL: Atom .R<ILE 827>.A<OH 20> does not have a type.
> FATAL: Atom .R<ILE 827>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 827>.A<CE1 22> does not have a type.
> FATAL: Atom .R<ILE 835>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 837>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 845>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 847>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 847>.A<CE1 21> does not have a type.
> FATAL: Atom .R<ILE 849>.A<CD2 20> does not have a type.
> FATAL: Atom .R<ILE 849>.A<CE2 21> does not have a type.
> FATAL: Atom .R<ILE 849>.A<CG 22> does not have a type.
> FATAL: Atom .R<ILE 851>.A<CE1 20> does not have a type.
> FATAL: Atom .R<ILE 851>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 853>.A<CE2 20> does not have a type.
> FATAL: Atom .R<ILE 853>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 853>.A<CD2 22> does not have a type.
> FATAL: Atom .R<ILE 855>.A<CZ 20> does not have a type.
> FATAL: Atom .R<ILE 855>.A<CE1 21> does not have a type.
> FATAL: Atom .R<ILE 855>.A<CE2 22> does not have a type.
> FATAL: Atom .R<ILE 863>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 865>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 865>.A<CE1 21> does not have a type.
> FATAL: Atom .R<ILE 867>.A<CD2 20> does not have a type.
> FATAL: Atom .R<ILE 867>.A<CE2 21> does not have a type.
> FATAL: Atom .R<ILE 867>.A<CG 22> does not have a type.
> FATAL: Atom .R<ILE 869>.A<CE1 20> does not have a type.
> FATAL: Atom .R<ILE 869>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 871>.A<CE2 20> does not have a type.
> FATAL: Atom .R<ILE 871>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 871>.A<CD2 22> does not have a type.
> FATAL: Atom .R<ILE 873>.A<OH 20> does not have a type.
> FATAL: Atom .R<ILE 873>.A<CZ 21> does not have a type.
> FATAL: Atom .R<ILE 873>.A<CE1 22> does not have a type.
> FATAL: Atom .R<ILE 881>.A<SG 20> does not have a type.
> FATAL: Atom .R<ILE 889>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 891>.A<OG 20> does not have a type.
> FATAL: Atom .R<ILE 896>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 898>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 898>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 900>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 900>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 908>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 910>.A<CD2 20> does not have a type.
> FATAL: Atom .R<ILE 910>.A<NE2 21> does not have a type.
> FATAL: Atom .R<ILE 910>.A<CG 22> does not have a type.
> FATAL: Atom .R<ILE 912>.A<CE1 20> does not have a type.
> FATAL: Atom .R<ILE 912>.A<ND1 21> does not have a type.
> FATAL: Atom .R<ILE 912>.A<NE2 22> does not have a type.
> FATAL: Atom .R<ILE 914>.A<NE2 20> does not have a type.
> FATAL: Atom .R<ILE 914>.A<CE1 21> does not have a type.
> FATAL: Atom .R<ILE 914>.A<CD2 22> does not have a type.
> FATAL: Atom .R<ILE 922>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 924>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 924>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 926>.A<NE2 20> does not have a type.
> FATAL: Atom .R<ILE 926>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 926>.A<CG 22> does not have a type.
> FATAL: Atom .R<ILE 926>.A<OE1 23> does not have a type.
> FATAL: Atom .R<MEM 948>.A<N 1> does not have a type.
> FATAL: Atom .R<MEM 951>.A<H 1> does not have a type.
> FATAL: Atom .R<MEM 951>.A<CA 2> does not have a type.
> FATAL: Atom .R<MEM 953>.A<HA 1> does not have a type.
> FATAL: Atom .R<MEM 953>.A<C 2> does not have a type.
> FATAL: Atom .R<MEM 953>.A<O 3> does not have a type.
> FATAL: Atom .R<MEM 953>.A<CB 4> does not have a type.
> FATAL: Atom .R<ILE 954>.A<CG 20> does not have a type.
> FATAL: Atom .R<MEM 955>.A<HB3 1> does not have a type.
> FATAL: Atom .R<MEM 955>.A<HB2 2> does not have a type.
> FATAL: Atom .R<MEM 955>.A<CG 3> does not have a type.
> FATAL: Atom .R<ILE 956>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 956>.A<SD 21> does not have a type.
> FATAL: Atom .R<MEM 957>.A<HG3 1> does not have a type.
> FATAL: Atom .R<MEM 957>.A<HG2 2> does not have a type.
> FATAL: Atom .R<MEM 957>.A<SD 3> does not have a type.
> FATAL: Atom .R<MEM 957>.A<CE 4> does not have a type.
> FATAL: Atom .R<ILE 958>.A<CE 20> does not have a type.
> FATAL: Atom .R<ILE 958>.A<SD 21> does not have a type.
> FATAL: Atom .R<ILE 958>.A<CG 22> does not have a type.
> FATAL: Atom .R<MEM 959>.A<HE1 1> does not have a type.
> FATAL: Atom .R<MEM 959>.A<HE2 2> does not have a type.
> FATAL: Atom .R<MEM 959>.A<HE3 3> does not have a type.
> FATAL: Atom .R<ILE 984>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 986>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 986>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 988>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 988>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 988>.A<CE 22> does not have a type.
> FATAL: Atom .R<ILE 990>.A<CE 20> does not have a type.
> FATAL: Atom .R<ILE 990>.A<CD 21> does not have a type.
> FATAL: Atom .R<ILE 990>.A<NZ 22> does not have a type.
> FATAL: Atom .R<ILE 992>.A<NZ 20> does not have a type.
> FATAL: Atom .R<ILE 992>.A<CE 21> does not have a type.
> FATAL: Atom .R<ILE 992>.A<CD 22> does not have a type.
> FATAL: Atom .R<ILE 1012>.A<OG1 20> does not have a type.
> FATAL: Atom .R<ILE 1014>.A<OG1 20> does not have a type.
> FATAL: Atom .R<ILE 1036>.A<CG 20> does not have a type.
> FATAL: Atom .R<ILE 1038>.A<ND2 20> does not have a type.
> FATAL: Atom .R<ILE 1038>.A<CG 21> does not have a type.
> FATAL: Atom .R<ILE 1038>.A<OD1 22> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> >
>
> I don't understand where the problem is. Could someone help me please? Thank
> you.

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++

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