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.yahoo.com> wrote:
>
> > Date: Fri, 23 Nov 2007 00:15:05 -0800 (PST)
> > From: Francesco Pietra <chiendarret.yahoo.com>
> > Subject: About TER records
> > To: Amber <amber.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
---------------------------------------------------------------
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= University of Rochester - =
= Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
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Received on Sun Nov 25 2007 - 06:07:38 PST
