RE: [gmx-users] which force file has parameters for creatine md simulations

2010-11-05 Thread #ZHAO LINA# 
http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Olga Ivchenko [olga.ivche...@gmail.com]
Sent: Friday, November 05, 2010 6:02 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] which force file has parameters for creatine md simulations

Dear All,

I want to do molecular dynamics with creatine. But I can not transform creatine 
pdb file downloaded from drugbank to gromac topology file using command: 
pdb2gmx -f

Please can you write me if there is a force filed for which creatine parameters 
are already exist and I can use this forcefield for simulations?

I have attached pdb file.

Thanks in advance,
Olga
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Re: [gmx-users] which force file has parameters for creatine md simulations

2010-11-05 Thread Justin A. Lemkul 



#ZHAO LINA# wrote:

http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta



The usual caveat applies:

http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips

The raw output of PRODRG is often quite unsatisfactory and inconsistent with any 
Gromos96 parameter set.


-Justin


lina

*From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on 
behalf of Olga Ivchenko [olga.ivche...@gmail.com]

*Sent:* Friday, November 05, 2010 6:02 PM
*To:* gmx-users@gromacs.org
*Subject:* [gmx-users] which force file has parameters for creatine md 
simulations


Dear All,

I want to do molecular dynamics with creatine. But I can not transform 
creatine pdb file downloaded from drugbank to gromac topology file using 
command: pdb2gmx -f


Please can you write me if there is a force filed for which creatine 
parameters are already exist and I can use this forcefield for simulations?


I have attached pdb file.

Thanks in advance,
Olga



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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