[gmx-users] Re: pdb2gmx error

[shounakb]

sorry about  the previous post! I have not yet looked at the code for pdb2gmx
(and a lot of other stuff).
I think the formyl-valine idea is pretty cool and found this thread very
informative.
Thank you!
Shounak

Justin A. Lemkul wrote
> 
> 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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>>
>>
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>>
> 
> -- 
> ========================================
> 
> 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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