On 5/18/13 10:02 AM, Shima Arasteh wrote:
Hi all,
I want to add CS ions to my system by genion but it seems impossible when go
through the EM.
The molecule section in my top file is:
Protein_chain_A 1
Protein_chain_B 1
POPC 238
SOL 20406
NA 681
CL 702
CS 19
The commands to neutralize and adding CsCl are as follow:
Adding ions:
#grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr
#genion -s ions.tpr -o system_solv_ions.gro -p topol.top -conc 1 -neutral
Adding 19 pairs of CsCl:
#grompp -f ions.mdp -c system_solv_ions.gro -p topol.top -o ions_CsCl.tpr
#genion -s ions_CsCl.tpr -o system_solv_ions_CsCl.gro -p topol.top -pname CS
-np 19 -nname CL -nn 19
EM:
And fatal error as I get is:
#grompp -f minim.mdp -c system_solv_ions_CsCl.gro -p topol.top -o minim.tpr
Fatal error:
No such moleculetype CS
But I see the CS ion in residuetypes.dat which exist in my directory :
CS Ion
So what's the reason? If it is related to the version of applied GROMACS? I am
working with 4.5.5 GROMACS and CHARMM 36 FF.
All that residuetypes.dat indicates is that Gromacs, in general, has the ability
to understand that Cs are ions. That is not to say that every force field has
parameters for Cs. That's your problem - the CHARMM force field you have
doesn't include parameters for a moleculetype named "CS" (look at its ions.itp
file), though CHARMM27 packaged with Gromacs does have these parameters.
-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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