AMBER Archive (2007)

Subject: Re: AMBER: Fwd: [chirality.c] Atom did not match

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat Nov 17 2007 - 04:56:01 CST

Thanks, please see below.

--- "David A. Case" <case_at_scripps.edu> wrote:

> On Fri, Nov 16, 2007, Francesco Pietra wrote:
>
> > I further checked that step (4) below does not give problems when loading a
> > single POPC molecule:
> >
> > model = loadpdb "popc.pdb"
> >
> > edit model
> >
> > May it be that problems to leap (and not to either VMD or Chimera) arise
> from
> > how membrane.pdb is written, i.e. without TER records separating the
> various
> > molecules?
>
> Not having TER cards in the proper place will certainly lead to bad things
> inside leap, and "chirality" problems are likely to one of them, since LEaP
> is
> likley to try to create bonds between chains if TER cards are not present.
>
> ...dac

Yes, placing TER removed the problem. However, the membrane also contains TIP3
water, which now appears in the pbd file - after the last POPC, as follows:
ATOM 50276 H16Z POPC 1 43.269 47.258 4.049 1.00 0.00 L29 H
TER
ATOM 50277 OH2 TIP3 307 47.752 43.891 17.330 1.00 0.00 W45 O
ATOM 50278 H1 TIP3 307 46.913 43.577 17.668 1.00 0.00 W45 H
ATOM 50279 H2 TIP3 307 48.403 43.284 17.681 1.00 0.00 W45 H
ATOM 50280 OH2 TIP3 329 48.920 45.324 20.742 1.00 0.00 W45 O
ATOM 50281 H1 TIP3 329 48.993 45.140 21.678 1.00 0.00 W45 H
ATOM 50282 H2 TIP3 329 48.108 44.897 20.469 1.00 0.00 W45 H
ATOM 50283 OH2 TIP3 436 47.190 47.077 22.860 1.00 0.00 W45 O
ATOM 50284 H1 TIP3 436 47.849 47.025 22.168 1.00 0.00 W45 H
ATOM 50285 H2 TIP3 436 46.659 47.843 22.641 1.00 0.00 W45 H
ATOM 50286 OH2 TIP3 485 46.681 43.291 14.229 1.00 0.00 W45 O
ATOM 50287 H1 TIP3 485 46.447 43.821 13.467 1.00 0.00 W45 H
ATOM 50288 H2 TIP3 485 45.989 43.456 14.868 1.00 0.00 W45 H
ATOM 50289 OH2 TIP3 491 46.993 43.169 26.500 1.00 0.00 W45 O
ATOM 50290 H1 TIP3 491 47.389 43.133 27.370 1.00 0.00 W45 H
ATOM 50291 H2 TIP3 491 46.079 43.408 26.653 1.00 0.00 W45 H
ATOM 50292 OH2 TIP3 760 46.046 49.255 16.105 1.00 0.00 W45 O
ATOM 50293 H1 TIP3 760 46.556 50.049 15.943 1.00 0.00 W45 H
ATOM 50294 H2 TIP3 760 46.285 48.983 16.991 1.00 0.00 W45 H
ATOM 50295 OH2 TIP3 763 47.196 43.412 -19.903 1.00 0.00 W45 O
ATOM 50296 H1 TIP3 763 47.413 42.941 -20.708 1.00 0.00 W45 H
ATOM 50297 H2 TIP3 763 46.883 42.738 -19.299 1.00 0.00 W45 H
ATOM 50298 OH2 TIP3 1057 47.946 46.153 -21.523 1.00 0.00 W45 O
ATOM 50299 H1 TIP3 1057 48.230 45.975 -22.420 1.00 0.00 W45 H
ATOM 50300 H2 TIP3 1057 47.602 45.320 -21.202 1.00 0.00 W45 H
ATOM 50301 OH2 TIP3 1610 45.043 43.854 -14.517 1.00 0.00 W45 O
ATOM 50302 H1 TIP3 1610 44.236 44.347 -14.665 1.00 0.00 W45 H
ATOM 50303 H2 TIP3 1610 44.813 43.196 -13.860 1.00 0.00 W45 H
ATOM 50304 OH2 TIP3 1687 46.137 48.009 -23.496 1.00 0.00 W45 O
ATOM 50305 H1 TIP3 1687 46.426 47.930 -22.587 1.00 0.00 W45 H
ATOM 50306 H2 TIP3 1687 45.223 47.724 -23.491 1.00 0.00 W45 H
ATOM 50307 OH2 TIP3 1720 48.320 49.994 23.169 1.00 0.00 W45 O
ATOM 50308 H1 TIP3 1720 47.808 50.201 23.951 1.00 0.00 W45 H
ATOM 50309 H2 TIP3 1720 49.059 49.475 23.487 1.00 0.00 W45 H
ATOM 50310 OH2 TIP3 1730 45.757 47.739 25.647 1.00 0.00 W45 O
ATOM 50311 H1 TIP3 1730 46.532 47.301 25.294 1.00 0.00 W45 H
ATOM 50312 H2 TIP3 1730 45.585 47.304 26.481 1.00 0.00 W45 H
ATOM 50313 OH2 TIP3 2223 45.853 44.598 -23.501 1.00 0.00 W45 O
ATOM 50314 H1 TIP3 2223 46.797 44.454 -23.557 1.00 0.00 W45 H
ATOM 50315 H2 TIP3 2223 45.663 44.638 -22.564 1.00 0.00 W45 H
ATOM 50316 OH2 TIP3 3357 47.120 46.103 -26.069 1.00 0.00 W45 O
ATOM 50317 H1 TIP3 3357 46.727 45.819 -26.895 1.00 0.00 W45 H
ATOM 50318 H2 TIP3 3357 47.214 47.052 -26.153 1.00 0.00 W45 H
END

That format is disliked by leap, or parameters are missing. If you are patient
enough (or interested), what I did (in detail because this is my first time in
such affairs):

(1)Load leaprc.ff99SB and leaprc.gaff into xleap.
(2) loadamberprep popc.prepin.
(3)loadamberparams popc.frcmod (which was actually redundant because
Antechamber had no problems with POPC).
(4) model_mem = loadpdb "membrane.pdb"
(5) model_myprotein = loadpdb "myprotein.pdb"
(6) myprotein_popc = combine {model_mem model_myprotein}
(I choose combine rather than sequence because present attempts are a
simplification of my final aim, involving myprotein with a docked ligand coming
from DOCK6.1)
(7) saveamberparm myprotein_popc p_p.prmtop p_p.inpcrd
 which failed because (reporting the last of the FATAL issues):
FATAL: Atom .R<TIP 61>.A<OH2 1> does not have a type.

My understanding is that I should have provided parameters for the water in
the membrane. Though, I was unable to find how they could be provided. An
alternative is to remove all TIP3 from the membrane.pdb. And solvate with water
thereafter. Surely that will pass through leap, however, I fear that the
membrane constructed with VMD would suffer heavily.

There may also be a problem with the single (natural) HOH residue inside the
protein, which again appears in xleap with H-H bond. I had resolved that issue
(dock-fans list). Maybe it is here again. Though, I have first to solve the
above issues.

Thanks
francesco

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