Liu Shiyong wrote:
command:
+ pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro
+ pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb
+ editconf -f a6.gro -o a6.gro -d 20.0
+ make_ndx -f a.pdb -o a6.ndx
+ grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr
I think you still don't need two invocations of pdb2gmx. Your only
constraint is that you want chain IDs preserved for your make_ndx
command. The PDB format carries the system size just like the GRO
format. Thus
+ pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb
+ editconf -f a6.pdb -o a6.gro -d 20.0
+ make_ndx -f a6.pdb -o a6.ndx
+ grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr
Simpler still is to define your index groups using information other
than the chain ID - as I think someone suggested days ago. Ranges of
atom numbers are also effective.
-------------------------------------------------------
Program grompp, VERSION 4.0.2
Source code file: grompp.c, line: 150
Fatal error:
atoms 1 and 2 in charge group 1 of molecule type
'Protein_A' are
in different energy groups
-------------------------------------------------------
There is still some sort of disconnect between topology numbering
(which is where charge groups are defined), and the structure you
are using. Can you post the first *few* lines of your .pdb file, [
atoms ] section of the .top, and the relevant index groups?
Not necessarily - the assignment of energy groups in the .mdp file is
still a potential source of problems.
Mark
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