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hi all,<br>
i am using this template of commands to remove the solvent molecules from the xtc file.but i found that the solvent molecues are not being deleted from the xtc file.The trajectory shows distorted image in vmd when loaded on pdb file but works fine when loaded on .gro file which also has solvent molecules.(either way of no use).All trajectories run well on ngmx(with and without solvent molecules).<br>
(procedure adapted as per a "reply" by Dr.Warren in the gromacs archives).<br>
<br>
trjconv_mpi -f viimd.trr -o viimd.xtc<br>
<br>
make_ndx_mpi -f conf.gro -o index.ndx<br>
(In this option i chose protein)<br>
<br>
trjconv_mpi -f viimd.xtc -o ready.xtc -s 1BXL-bclxl-bak-complex.pdb -n index.ndx<br>
<br>
Can anyone please help me on this as I have some ten trajectory files with the same problem.<br>
Thanks in advance.<br>
cheers<br>
hayagreevan
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