Anirban Ghosh wrote:
Hi,
I have successfully converted my CG (only) protein model to FG model
using g_fg2cg command of the gromacs_reverse package. But now when I try
to compile my .mdp file for SA run, grompp is throwing some warnings:
creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
WARNING 1 [file fg_protein.mdp, line unknown]:
Unknown left-hand 'cap_force' in parameter file
WARNING 2 [file fg_protein.mdp, line unknown]:
Unknown left-hand 'cap_a' in parameter file
WARNING 3 [file fg_protein.mdp, line unknown]:
Unknown left-hand 'fc_restr' in parameter file
WARNING 4 [file fg_protein.mdp, line unknown]:
Unknown left-hand 'r_CGW' in parameter file
WARNING 5 [file fg_protein.mdp, line unknown]:
Unknown left-hand 'fc_restrW' in parameter file
WARNING 6 [file fg_protein.mdp, line unknown]:
Unknown left-hand 'rel_steps' in parameter file
WARNING 7 [file fg_protein.mdp, line unknown]:
Unknown left-hand 'rel_water' in parameter file
checking input for internal consistency...
calling /lib/cpp...
processing topology...
---------------------------------------------------------------------------------------------------------
My system contains only multiple copies of a protein. How to solve this
issue?
Any suggestion is welcome.
Use proper .mdp settings. You're being told that your "fg_protein.mdp" contains
numerous keywords that do not exist in normal Gromacs.
-Justin
Thanks,
-Anirban
--
========================================
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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