> when I visualize generated com.pdb file by VMD, attached figure is created.
> in that water, Na+, DNA are good and normal but protein is unusual
> (1- there is no connection between residues. 2- hydrogen atoms are as dot
> and didn't connect to other atoms. 3- there are undesirable bonds between
> atoms)
The pdb generated by ambpdb doesn't have CONECT records, so the
display program is left to guess which bonds to draw. The only
use of such a pdb in the current case is to make sure the atom order
corresponds to your Gromacs trajectory. If it doesn't, you may need to
process your Gromacs trajectory to rearrange the coordinates before
analyzing in Amber.
Bill
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Received on Mon Dec 13 2010 - 11:30:03 PST
