Thnx for replying A] 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.
B] 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. C] 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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