AMBER Archive (2007)

Subject: Re: AMBER: Fwd: About TER records

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat Nov 24 2007 - 15:27:11 CST


Removing all CONECTs from the edited file described below made a Lead-palatable
pdb file.

Finally! Although the way is still long. I have become accustomed to have
another problem soon as present one is solved.

francesco
 
--- Francesco Pietra <chiendarret_at_yahoo.com> wrote:

> Ilyas:
> Still in the dark.
>
> The membrane file from VMD is OK for Leap after a few modifications:
>
> Insert all TERs, TIP3 -> WAT, OH2 -> O
>
>
> When I create a cavity in the membrane for the protein using Chimera, and I
> edit the residues as they are in the above, i.e.
>
> HETATM -> ATOM, label for single-character atom names at column 13 when there
> are four characters, e.g. 2C21 -> C212 or SH11 -> H11S, still it does not
> work.
> leap.log ends with:
>
> Added missing heavy atom: .R<POP 2044>.A<C211 23>
> Added missing heavy atom: .R<POP 2045>.A<C314 125>
> Added missing heavy atom: .R<POP 2045>.A<C211 23>
> Added missing heavy atom: .R<POP 2046>.A<C314 125>
> Added missing heavy atom: .R<POP 2046>.A<C211 23>
> Bond: Maximum coordination exceeded on .R<POP 1>.A<H11R 24>
> -- setting atoms pert=true overrides default limits
> ATOMS NOT BONDED: .R<POP 1>.A<C210 26> .R<POP 1>.A<H11R 24>
>
> It is true that prepin for the lipid is for POP, while the residue name in
> pdb
> is named POPC, but that works with the intact membrane.
>
> The only macroscopic difference I notice in the membrane pdb from Chimera
> (the
> one with cavity), is the absence of segID that VMD placed for both the lipid
> and water that solvates the polar head, and the presence of CONECTs that VMD
> did not place.
>
> Letting Chimera write a pdb file is getting headache. In their aim to follow
> the latest PDB rules, they certainly have a bug: the way they write hydrogens
> with four characters, see above. Hydrogen overrides the latest rules for the
> other on-character elements as to column positioning.
>
> Thanks
> francesco
>
>
> --- Ilyas Yildirim <yildirim_at_pas.rochester.edu> wrote:
>
> > Francesco,
> >
> > When I prepare prmtop/inpcrd files, I replace all the HETATM to ATOM.
> > Replace HETATM with ATOM and if you have prepared the library files
> > correct, you should not have any serious problems. The .pdb files should
> > be in Brookhaven pdb format (for more on the .pdb format, go to
> > www.pdb.org website).
> >
> > Best,
> >
> > On Fri, 23 Nov 2007, Francesco Pietra wrote:
> >
> > > Problems are more serious than anticipated in my original email (reported
> > at
> > > the bottom).
> > >
> > > A 80x80A POPC/WAT membrane pdb that was accepted by Leap to get top/crd,
> > once
> > > passed through Chimera is no more good. Why through Chimera? To carry out
> > > processes that Leap can't do.
> > >
> > > All TER were removed by Chimera, and ATOM renamed HETATM, while CONECT
> > records
> > > were added.
> > >
> > > As such, Leap said:
> > > In file [chirality.c], line 142
> > > Atom named C217 from POP did not match
> > > Aborting
> > >
> > > I knew such type of message. There is no C217 atom. On previous
> (different)
> > > occasions, insertion of TER records put the house in order.
> > >
> > > I inserted all TERs between POPC residues and between WAT residues.
> > >
> > > Now Leap said:
> > > In file [atom.c], line 444
> > > bond AtomProblem found
> > > Aborting
> > >
> > > As I did not knew this type of message, I tried to investigate that line
> > 444.
> > > According to vim
> > >
> > > :n,444
> > >
> > > that line, indicated at bottom ot terminal as "444,1", reads
> > >
> > > HETATM 441 O31 POPC 5 -44.082 -12.831 14.685 1.00 0.00
>
> > O
> > >
> > >
> > > A carbon atom (if "[atom.c]" means carbon, is at line 447,1, which reads
> > >
> > > HETATM 444 C32 POPC 5 -46.343 -12.925 15.140 1.00 0.00
>
> > C
> > >
> > >
> > > In the original (good) pdb those lines read:
> > >
> > > ATOM 441 O31 POPC 4 -37.722 -19.453 18.019 1.00 0.00
> L11
> > O
> > >
> > > ATOM 444 C32 POPC 4 -39.844 -19.273 18.941 1.00 0.00
> L11
> > C
> > >
> > >
> > > Worse, Chimera changed the atom names, like in the final part of the POPC
> > > residue
> > >
> > > HETATM 528 XH14 POPC 5 -47.646 -9.424 -0.112 1.00 0.00
>
> > H
> > > HETATM 529 YH14 POPC 5 -46.217 -10.553 -0.172 1.00 0.00
>
> > H
> > > HETATM 530 5C31 POPC 5 -47.890 -11.168 -1.419 1.00 0.00
>
> > C
> > > HETATM 531 XH15 POPC 5 -47.763 -12.309 -1.296 1.00 0.00
>
> > H
> > > HETATM 532 YH15 POPC 5 -48.986 -11.063 -1.417 1.00 0.00
>
> > H
> > > HETATM 533 6C31 POPC 5 -47.242 -10.566 -2.756 1.00 0.00
>
> > C
> > > HETATM 534 XH16 POPC 5 -46.135 -10.759 -2.831 1.00 0.00
>
> > H
> > > HETATM 535 YH16 POPC 5 -47.802 -11.112 -3.597 1.00 0.00
>
> > H
> > > HETATM 536 ZH16 POPC 5 -47.451 -9.454 -2.737 1.00 0.00
>
> > H
> > > TER
> > >
> > >
> > > which, in the original (good) pdb was:
> > >
> > > ATOM 528 H14X POPC 4 -38.665 -14.879 4.398 1.00 0.00
> L11
> > H
> > > ATOM 529 H14Y POPC 4 -39.080 -16.603 3.952 1.00 0.00
> L11
> > H
> > > ATOM 530 C315 POPC 4 -40.370 -15.221 2.996 1.00 0.00
> L11
> > C
> > > ATOM 531 H15X POPC 4 -41.330 -15.752 3.099 1.00 0.00
> L11
> > H
> > > ATOM 532 H15Y POPC 4 -40.694 -14.148 3.019 1.00 0.00
> L11
> > H
> > > ATOM 533 C316 POPC 4 -39.787 -15.573 1.664 1.00 0.00
> L11
> > C
> > > ATOM 534 H16X POPC 4 -39.553 -16.661 1.544 1.00 0.00
> L11
> > H
> > > ATOM 535 H16Y POPC 4 -40.534 -15.211 0.948 1.00 0.00
> L11
> > H
> > > ATOM 536 H16Z POPC 4 -38.782 -15.094 1.533 1.00 0.00
> L11
> > H
> > > TER
> > >
> > > As I am using the last (production) release of Chimera (against Amber9),
> I
> > > wonder which of the two is following the average pdb rules.
> > >
> > > It is very sad to have to waste time with such a babele.
> > >
> > > Thanks for help
> > > francesco pietra
> > >
> > >
> > >
> > >
> > > (the different coordinated because I made a hole in the membrane)
> > > --- Francesco Pietra <chiendarret_at_yahoo.com> wrote:
> > >
> > > > Date: Fri, 23 Nov 2007 00:15:05 -0800 (PST)
> > > > From: Francesco Pietra <chiendarret_at_yahoo.com>
> > > > Subject: About TER records
> > > > To: Amber <amber_at_scripps.edu>
> > > >
> > > > As I have to come to Amber9 with pdb files that have passed other
> > software
> > > > (DOCK, Chimera, VMD, MM packages) I would like to know which protocol
> is
> > > > followed by Amber9 at present about TER records.
> > > >
> > > > Precisely, which residues are termed ATOM and which ones HETATM, and
> > whether
> > > > TER records are always needed to separate different residues if called
> > ATOM,
> > > > while not necessary if called HETATM.
> > > >
> > > > For example, a pdb file only containing lipid and water molecules is
> > accepted
> > > > by LEaP with ATOM, while Chimera transforms all ATOM recods into HETATM
> > > > records
> > > > and removes all TER records that I had interposed between the lipid and
> > the
> > > > water residues. In fact, when LEaP solvates, it adds TER records
> between
> > the
> > > > water residues.
> > > >
> > > > If I remember correctly, recent pdb rules tell that it is technically
> > correct
> > > > to remove the TERs between HETATM residues because HETATM residues in
> PDB
> > > > format are not connected to each other unless there are CONECT records
> > that
> > > > say
> > > > the contrary.
> > > >
> > > > To be on the safe side, I always insert TERs. Though, they are removed
> by
> > > > other
> > > > packages. Luckily there is Python to rearrange the files. Annoying,
> > however,
> > > > and not free of problems if one is rushed.
> > > >
> > > > Thanks
> > > > francesco pietra
> > > >
> > > >
> > > >
> > > >
> > >
> >
>
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> > >
> > >
> > >
> >
>
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> >
> > --
> > Ilyas Yildirim
> > ---------------------------------------------------------------
> > = Department of Chemistry - =
> > = University of Rochester - =
> > = Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
> > = http://www.pas.rochester.edu/~yildirim/ =
> > ---------------------------------------------------------------
> >
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>
>
>
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