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.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.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
> > >
> > >
> > >
> > >
> >
>
____________________________________________________________________________________
> > > Be a better pen pal.
> > > Text or chat with friends inside Yahoo! Mail. See how.
> > > http://overview.mail.yahoo.com/
> > >
> >
> >
> >
> >
>
____________________________________________________________________________________
> > Be a better sports nut! Let your teams follow you
> > with Yahoo Mobile. Try it now.
> http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
> >
>
> --
> Ilyas Yildirim
> ---------------------------------------------------------------
> = Department of Chemistry - =
> = University of Rochester - =
> = Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
> = http://www.pas.rochester.edu/~yildirim/ =
> ---------------------------------------------------------------
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
____________________________________________________________________________________
Be a better sports nut! Let your teams follow you
with Yahoo Mobile. Try it now.
http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Nov 25 2007 - 06:07:57 PST
