On 2/28/2007 7:52 PM, Mark Abraham wrote:
Qiang Zhong wrote:
Dear users:
I want to prepare protein simulation on 0.15mol/l salt
concentration,I use
genion command to add ions,After genion,I change cln.top file last
line to NA+
61,CL- 41.
When I execute grompp ,there are warning :
Warning: atom names in cln.top and cln_b4em.gro don't match (CL - Na)
........
(more than 20 non-matching atom names)
WARNING 1 [file "cln.top", line 9059]:
102 non-matching atom names
atom names from cln.top will be used
atom names from cln_b4em.gro will be ignored
I continue to execute "mdrun nice 0 -v -s cln_em.tpr -o
minim_traj.trr -c
minimized.gro -e minim_ener.edr",There are some error:
Hardly surprising... most gromacs warnings should be considered
carefully.
I think what Mark means is that in such case, you shall not continue to
run mdrun without inspecting the warnings.
First the atom names in your .gro and .top files have to match those
in the .atp files for the force field you're using. Then check the
order and number of Na and Cl are correct.
Mark
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