[gmx-users] pdb2gmx with GROMOS

[Justin Lemkul]

It's because the GROMOS force fields are the only ones that explicitly list 
[angles] in the .rtp file.  All other force fields let these be generated 
automatically by the bonded structure; this is due to some subtle ways in which 
the force field files differ in their organization (use of #define for bonded 
parameters in GROMOS, etc).

So atoms get deleted when merging the .tdb hackblocks with the .rtp bondeds, 
triggering a warning that something has been deleted.  It causes no problem. 
Probably something subtle has changed, because I have never seen such warnings 
with GROMOS until recently, but these do not indicate any problem.  The bonded 
parameters change due to the altered atom types when creating termini, so the 
correct parameters should always be written.

-Justin

On 2/19/16 8:14 AM, Dries Van Rompaey wrote:
> 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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
==================================================

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

==================================================