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

[Justin Lemkul]

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

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