[gmx-users] selecting res CYS from G53a5 using pdb2gmx

[Payman Pirzadeh]

Dear Justin,
Thanks for your suggestions. It all made sense.
But I ran into a strange problem. I checked the mail list, and all I found
was about misspelling the force field name. I copied the whole gromos53a5.ff
directory into my working folder, copied the modified .rtp, .dat and .hdb
files into the gromos53a5.ff folder, and issued:
pdb2gmx_d_mpi -f protein.pdb -p protein-CYA.top -o protein-CYA.gro -inter
-ff gromos53a5.ff
but what I got was:

Program pdb2gmx_d_mpi, VERSION 4.5.4
Source code file: pdb2top.c, line: 239

Fatal error:
Could not find force field 'gromos53a5.ff' in current directory, install
tree or GMXDATA path.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

If I do not add the -ff option, the default pdb2gmx command works, by
opening the force field from the default path. I tried 'source GMXRC' from
my working folder, but same error pops up. I am not sure what I am missing
here?!
Sorry for mass of e-mails.

Payman 

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Justin Lemkul
Sent: January-07-13 5:43 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx



On 1/7/13 7:36 PM, Payman Pirzadeh wrote:
> Two clarifications:
> 1. can utilization of an index file help during topology generation 
> for my problem?

No.  Reading pdb2gmx -h will tell you this.

> 2. I use -inter for getting prompted for LYS, ARG, ... but CYS is not 
> one of them.

CYS should be one of the choices.  If you want to make your life really
easy, name your residue "CYA" instead of "CYSA" so that the selection
machinery never deals with it.  Make sure you have an appropriate .hdb entry
as well and pdb2gmx will do whatever you tell it.

-Justin

> Cheers,
>
> Payman
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Payman Pirzadeh
> Sent: January-07-13 5:28 PM
> To: 'Discussion list for GROMACS users'
> Subject: RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx
>
> Dear Justin,
> I have been able to temporarily solve my force field parameter problem  
> (at least test the new parameters). I defined a new Cys residue say 
> CYSA (as
> anion) in the rtp file. But how can I prevent the pdb2gmx from adding 
> hydrogen to the Cysteine residue? Addition of this extra hydrogen 
> changes all the indexing. Can utilization of an index file during 
> topology generation? or can "grompp -renum" help in this case?
> I am left wondered how to force pdb2gmx to prompt to ask me for the 
> selection of the type, when several types of a particular residue is 
> defined in the rtp file?
> Your help is appreciated in advance.
> Best,
>
> Payman
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Justin Lemkul
> Sent: January-06-13 6:54 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx
>
>
>
> On 1/6/13 4:45 PM, Payman Pirzadeh wrote:
>> Hi,
>> I am using gromacs 4.5.4, and I am generating a topology file using
>> G53a5 force field. My protein has a Cys residue which is supposed to 
>> be in thiolate state (negatively charged side chain). During issuing 
>> the pdb2gmx command I use the switch -inter to be prompted about the 
>> charge state of the ionisable side chains, but it asks nothing about 
>> Cys side chains except about they being involved in disulfide bonds.
>> My
> questions are:
>> 1. how can I get pdb2gmx ask me about the charge status of Cys 
>> residues? Or do I need to manually change their status in the 
>> topology file and output gro file (removing the HG)?
>> 2. I checked the aminoacid.rtp of G53a5, and it seems that for CYS, 
>> the total charge of the residue does not add to -1 but -0.5. Is 
>> anyone aware of any modifications to this force field parameters?
>
> I don't know of any.  The AMBER force fields have parameters for the 
> thiolate form of cysteine, but I've never seen them for Gromos96 force 
> fields.  That doesn't mean they don't exist, of course, but this is 
> the sort of thing one should research prior to choosing a force field 
> and then hoping for a solution later ;)
>
> -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
>
> ========================================
>

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

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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