[gmx-users] pdb2gmx with GROMOS

[Dries Van Rompaey]

That's good to know. Thanks for the clarifications.

On 19 February 2016 at 14:22, Justin Lemkul <jalemkul at vt.edu> wrote:

>
> 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
>>>
>>> ==================================================
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> --
> ==================================================
>
> 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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