Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private tutor. I am CC'ing this message there and ask that anything further
be posted to the list. See below for comments.
Zahra Kayani wrote:
Dear, Dr.Lemkul
command1:pdb2gmx -f shp2.pdb -o conf.gro it runs normally
then for g_x2top, I tried these focefield :
G53a5 GROMOS96 53a5 Forcefield (official distribution)
oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
but for both of them this error was appeared, now what should I do?
error: Could only find a forcefield type for 7351 out of 8397 atoms
please,tell which forcefield can be helpful for me.
The .n2t files that come pre-packaged with these force fields are largely
incomplete. Further, g_x2top is designed for small molecules, and for anything
complex, it may not be possible to define proper (non-conflicting) .n2t entries.
If you can get the topology via pdb2gmx, then you shouldn't have to do
anything else.
-Justin
with regards
Zahra
--
========================================
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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