[gmx-users] Re: pdb2gmx error

[Justin A. Lemkul]

On 6/27/12 2:49 PM, shounakb wrote:
> Hi Shima,
>      i do not think pdb2gmx uses the tdb files. However, I feel that the FOR
> tdb entries should go to aminoacids.c.tdb and not aminoacids.n.tdb
>

Both of these assertions are incorrect.  The *only* Gromacs program that uses 
.tdb files is pdb2gmx.  The FOR cap is on the N-terminus, so it cannot be in 
.c.tdb.  Both .tdb files are irrelevant for this problem, as stated before.

> I saw your other thread where you have described the FOR topology you added.
> I think the atoms should be CA and O and their respective atom types,
> CH1/CH2 and O.
>

This does not solve the problem.  If one changes the "C" atom name to "CA" then 
pdb2gmx will certainly complain that the atom "C" is missing, since improper 
construction for VAL is dependent upon atoms "C" and "CA" being present in the 
preceding residue.

> I guess you already have partial charges for the atoms? Shouldn't that solve
> the problem with VAL that Justin highlighted, without having to comment out
> the impropers line?
>

Partial charges are irrelevant here.  The error complains about an atom not 
being found, not the charge on any given atom.  Shima has a functional .rtp 
entry for the FOR residue.  It is not the problem, VAL is.  Better stated, the 
mechanism used by gmx.ff to generate impropers in this case blocks the use of 
FOR as a separate residue, since it does not contain the same atoms as an amino 
acid, specifically a C and CA.

-Justin

> Regards,
> Shounak
>
>
> Shima Arasteh wrote
>>
>> :))
>> I can't eliminate it, I decided to do , but when I studied about the
>> structure of protein ( consists of 2 monomers, which form a dimer in lipid
>> bilayer, and the reason of this formation is the existence of formyl
>> residues in N-teminals) . Then I got regretful to remove it. Don't you
>> agree?
>>
>>
>> Sincerely,
>> Shima
>>
>>
>> ----- Original Message -----
>> From: Justin A. Lemkul <jalemkul@>
>> To: Discussion list for GROMACS users <gmx-users@>
>> Cc:
>> Sent: Wednesday, June 27, 2012 10:25 PM
>> Subject: Re: [gmx-users] Re: pdb2gmx error
>>
>>
>>
>> On 6/27/12 1:52 PM, shounakb wrote:
>>> Shima, I use gromacs-4.5.4. Without the FOR residue, my
>>> gmx.ff/aminoacids.rtp
>>> file works fine for the sequence you originally specified. (pdb2gmx
>>> executes
>>> without any errors)
>>> I guess you added the FOR cap's topology yourself?
>>>
>>> Justin, could this be an issue?
>>>
>>
>> Please see the previous posts on these topics, including the post from
>> just a few minutes ago where I discovered the source of the problem.  The
>> FOR residue issue has been an ongoing discussion over several weeks.  I
>> will maintain that I do not necessarily believe that a two-atom model of a
>> formyl group is sufficiently accurate for a Gromos force field, since the
>> alpha proton is very polar and thus may need to be explicitly
>> represented.  I have stated my skepticism before but it appears Shima is
>> pursuing the current course.  Side note ;)
>>
>> -Justin
>>
>> -- ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>>
>>
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>
>
> --
> View this message in context: http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998870.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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