Dear AMBER,
I am calculating rmsd for my system by comparing it to reference structure (
.pdb). The pdb file created using ambpdb on the restart and prmtop file.
However, when I checked the atom names, some of them are different from
prmtop file, eg:
RG
.prmtop .pdb
atom H21 1H2
atom H22 2H2
Will this effect the ptraj to do rmsd? Or should I change the atom names in
pdb file to be similar to prmtop file?
Can I use restart file as reference structure?
Thanks.
Regards,
Siti
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Received on Mon Jan 17 2011 - 21:00:07 PST
