[gmx-users] Re: pdb2gmx error

[shounakb]

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

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.

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?

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
> 
> ========================================
> 
> 
> -- gmx-users mailing list    gmx-users@
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages are allowed!
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at .
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> --
> gmx-users mailing list    gmx-users@
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages are allowed!
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at .
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 


--
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.