AMBER Archive (2009)

Subject: Re: [AMBER] Trouble saving amberparm files

From: Tom Joseph (ttjoseph_at_gmail.com)
Date: Mon Jul 13 2009 - 16:13:14 CDT

Ah, I should have looked more closely. It seems like the names of your
hydrogens (HN, HB1, HG1, etc.) do not match those in ff99, which is
why leap doesn't know what to do with them. You should be able to
delete them from the PDB file and leap will automatically add them
back again with the correct names.

(You may also wish to reconsider using ff99 to begin with; it has been
deprecated. ff99SB is a better choice.)

--Tom

On Mon, Jul 13, 2009 at 5:06 PM, Alison
Saunders<alison.m.saunders_at_gmail.com> wrote:
> I did specify a force field: ff99.
>
> On Mon, Jul 13, 2009 at 1:16 PM, Tom Joseph <ttjoseph_at_gmail.com> wrote:
>
>> Did you specify a force field when invoking leap?
>>
>> --Tom
>>
>> > Hello,
>> >
>> > Here is part of my pdb file:
>> - snip! -
>> >
>> >
>> > I added Na+ ions in xleap to neautralize it, and I used solvatebox to put
>> it
>> > in water. My trouble comes when I try to saveamberparm. I get the errors:
>> >
>> >
>> >
>> > FATAL:  Atom .R<NMET 0>.A<HN 20> does not have a type.
>> > FATAL:  Atom .R<NMET 0>.A<HB1 21> does not have a type.
>> > FATAL:  Atom .R<NMET 0>.A<HG1 22> does not have a type.
>> > FATAL:  Atom .R<GLN 1>.A<HN 18> does not have a type.
>> > FATAL:  Atom .R<GLN 1>.A<HB1 19> does not have a type.
>> > FATAL:  Atom .R<GLN 1>.A<HG1 20> does not have a type.
>> > FATAL:  Atom .R<ALA 2>.A<HN 11> does not have a type.
>> > FATAL:  Atom .R<MET 3>.A<HN 18> does not have a type.
>> > FATAL:  Atom .R<MET 3>.A<HB1 19> does not have a type.
>> > FATAL:  Atom .R<MET 3>.A<HG1 20> does not have a type.
>> > FATAL:  Atom .R<ILE 4>.A<HN 20> does not have a type.
>> > FATAL:  Atom .R<ILE 4>.A<HG11 21> does not have a type.
>> > FATAL:  Atom .R<ALA 5>.A<HN 11> does not have a type.
>> > FATAL:  Atom .R<VAL 6>.A<HN 17> does not have a type.
>> > FATAL:  Atom .R<ALA 7>.A<HN 11> does not have a type.
>> > FATAL:  Atom .R<SER 8>.A<HN 12> does not have a type.
>> > FATAL:  Atom .R<SER 8>.A<HB1 13> does not have a type.
>> > FATAL:  Atom .R<GLN 9>.A<HN 18> does not have a type.
>> > FATAL:  Atom .R<GLN 9>.A<HB1 19> does not have a type.
>> > FATAL:  Atom .R<GLN 9>.A<HG1 20> does not have a type.
>> > FATAL:  Atom .R<ILE 10>.A<HN 20> does not have a type.
>> > FATAL:  Atom .R<ILE 10>.A<HG11 21> does not have a type.
>> > FATAL:  Atom .R<SER 11>.A<HN 12> does not have a type.
>> > FATAL:  Atom .R<SER 11>.A<HB1 13> does not have a type.
>> > FATAL:  Atom .R<PRO 12>.A<HB1 15> does not have a type.
>> >
>> > etc. etc.
>> >
>> > Any ideas on how to fix this problem?
>> >
>> > Thanks!
>> > Alison Saunders
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER_at_ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
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