[gmx-users] Sanjay (Reg: grompp error)
jalemkul at vt.edu
Thu May 14 18:38:43 CEST 2015
On 5/14/15 2:25 AM, sanjay choubey wrote:
> hi, i am doing membrane simulation . While emedding protein using the command given below:
> grompp -f empty.mdp -c prot_mem.nowater.gro -p topol.top -o test.tpr
> I am getting the error:
> Fatal error:Atomtype CA not found
> i checked topology file as well as lipid.itp file CA is there.
> kindly suggest the solution.
Are we to assume that you're following the GROMOS96+Berger approach from my
tutorial? If you are, lipid.itp should not be used (directly) and any reference
to CA (which is a GROMOS87 atom type and thus is not part of GROMOS96, hence the
error) should be removed. If you're following my tutorial, follow it more
closely and you'll get a working force field.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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