[gmx-users] pdb2gmx with GROMOS

Dries Van Rompaey dries.vanrompaey at gmail.com
Fri Feb 19 14:14:55 CET 2016


Sure. I pasted my original mail at the bottom.
I also followed your suggestion of trying the gromacs-master ff files, with
identical results. What I'm trying to find out is why the warning is being
triggered and if it's affecting the output in any way. My input is the 1AKI
pdb file as downloaded from the pdb. I'm converting it to .gro with the
command gmx pdb2gmx -f 1AKI.pdb, selecting the gromos54a7 force field with
spc waters.

Dear gmx-users,

I'm experiencing the following warning while running pdb2gmx (gmx pdb2gmx
-f 1AKI.pdb), selecting any of the GROMOS force fields; all others work
fine. I get the same error with the -ignh flag.

WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was
mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

WARNING: WARNING: Residue 129 named LEU of a molecule in the input file was
mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.

I'm using gromacs 5.1.1 on mac os x. I looked at the rtp and
aminoacids.c.tbd/aminoacids.n.tbd files in top/gromos54A7, but I couldn't
discover any discrepancies. I also checked the angles in the topology, but
it looks like everything that should be applied, based on the contents of
the aminoacids.c.tbd/aminoacids.n.tbd files, seems to be applied.

 The system I'm working on is lysozyme (pdb code 1AKI). I'm assuming the
root cause of this warning is located somewhere in the
aminoacids.c.tbd/aminoacids.n.tbd files, as both residues are terminal
residues.

Can anyone replicate these warnings or does anyone know where they come
from?

Thanks in advance,

Dries



On 19 February 2016 at 14:06, Justin Lemkul <jalemkul at vt.edu> wrote:

>
> Can you remind me of the context here?  You've provided output files that
> indicate everything is fine.  If there's a problem with *input* please
> provide those files, the exact command and selections, etc.
>
> I recall there was some terminus issue, but I've replied to a few hundred
> posts since then...
>
> -Justin
>
> On 2/19/16 3:50 AM, Dries Van Rompaey wrote:
>
>> Hi Justin,
>>
>> Sorry for the late reply. Haven't had a chance to look at this yet. Could
>> you post your output files or compare the contents of yours to mine? I
>> chose Gromos 54a7 as my forcefield with the SPC water model. (command line
>> is gmx pdb2gmx -f 1aki.pdb).
>> I'd like to know if this is a cosmetic issue or if something else is going
>> on.
>>
>> My files can be found here:
>> https://www.dropbox.com/sh/uapy2vxcprn0uje/AAA1TLME4czf8recVgV7U3koa?dl=0
>>
>> Thanks
>>
>> Dries
>>
>> On 1/20/16 3:48 AM, Dries Van Rompaey wrote:
>>
>>> * Hi Justin and Marco,
>>>
>> *>>* Thanks for your reply. I get this behaviour when I specify the
>> default NH3+
>> *>* and COO- termini through -ter, as well as when I don't use the -ter
>> flag.
>> *>* Selecting the COOH terminus type removed the warning for the
>> C-terminus,
>> *>* but selecting the NH2 terminus type did't remove the warning for the
>> *>* N-terminus. That's not a very physiological state, however.
>> *>>* Can anyone replicate this error?
>> *>
>> I can't trigger the same with 5.1 or with current git master.  Try from a
>> fresh
>> install and make sure no one has messed with your force field files.
>>
>> -Justin
>>
>> --
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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