[gmx-users] Regarding Trjconv.and ligand -protein complex simulation.......

PAVAN PAYGHAN pavanapex at gmail.com
Tue Feb 2 06:50:46 CET 2010

Thnx for replying
As i hv mentioned previously that in  my simulation  g_rms suggests it has
some large peaks ,so applied trjconv with
-pbc nojump now ...
 there are no peaks in rmsd its oky but in vmd it showed that water is not
having defined box so how to tackle this situation......
1.which -pbc option u suggests for this situation
2.is it possible to use two -pbc options together?
3.is it possible to modify the .xtc that i have generated with -nojump
further to have defined box.

my next question is with gromacs version 3.3.2
 if im using NMR structure i need to give -ignh  option in pdb2gmx to ignore
hydrogens or it will be taken care of  automatically.

 Will u please give me any tutorial on ligand-dna/protein simulation either
with PRODRG or ANTCHAMBER for drug input preparation.
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