prashant kurkute wrote:
Dear all,
I am very new to GROMACS.
The my problem may be a very basic and stupid but very big for me!!!!!!..
I am performing Justin Lemkul Lipid tutorial
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html)
and I am upto the 3rd stage.
But after giving following command
grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
I got the error like
Fatal error:
Atomtype CA not found
Please give me some valuable suggetion.
Read more closely:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html
"In the [ nonbond_params ] section, you will find the line ";; parameters for
lipid-GROMOS interactions." Delete this line and all of the subsequent lines in
this section. These nonbonded combinations are specific to the deprecated ffgmx
force field."
The CA atom type is from ffgmx, and hence the error.
-Justin
--
========================================
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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