Sangita Kachhap wrote:
Hello all
I am new for gromacs. I have to do MD simulation of membrane protein docked with
organic molecule.
I have gerated top and itp for ligand using PRODRG server also generated top
file for complex.
Hopefully you're not relying on an unrefined PRODRG topology. See the article
linked from:
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
But when I am generating .tpr file for a POPC system using grompp getting an
error:
creating statusfile for 1 node...
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Cleaning up temporary file gromppWQnjOb
Fatal error: Bond atom type names can't be single digits.
I am using gromacs-4.5.5
Can someone help me to find out where is actually problem is occuring?
It would help to see the topology, but based on a guess I would say that the
error is pretty explicit that you have atom types that are not appropriately
named; they are digits. Atom types can utilize numbers, but only as a part of
the name. For instance, CH3 is a valid atom type, but 3 is not.
-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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