pkmukher wrote:
Hi users,
I am having a problem during the running of the mdrun
program on my prepared system.I have a system containing a
protein/peptide complex. i have prepared the protein using
the pdb2gmx utility and the peptide using the PRODRG
utility. I have then included the ligand .itp
As has been suggested already, this is probably related to PBC, and
is in fact not a problem at all. Have you checked whether applying
the PBC puts the protein and peptide back together? Try out trjconv -
ur compact on your system and have a look at the output structure, or
run g_mindist to
Hi users,
I am having a problem during the running of the mdrun
program on my prepared system.I have a system containing a
protein/peptide complex. i have prepared the protein using
the pdb2gmx utility and the peptide using the PRODRG
utility. I have then included the ligand .itp file into the
pro
pkmukher wrote:
Mark and other users,
Thanks for the input. I understand that translation does
not have any effect on the energy calculations since the
point of reference is the protein itself.
The problem over here is that if a translation operation is
to be done it should perform the same op
Mark and other users,
Thanks for the input. I understand that translation does
not have any effect on the energy calculations since the
point of reference is the protein itself.
The problem over here is that if a translation operation is
to be done it should perform the same operation on all the
5 matches
Mail list logo
