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: [email protected] [mailto:[email protected]]
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: [email protected] [mailto:[email protected]]
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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