[gmx-users] Prot_prep_query

[pkmukher]

Hi,

  Thanks for your suggestions. I was using the 0 option
gromos FF in pdb2gmx. As you said the behavior is strange.
However i found a fix. I was using  a 2 step procedure

1) strip hydrogen > output pdb
2) input pdb > write output pdb with -inter flag

instead i used 

1) strip hydrogen > output pdb
2) input pdb > write pdb gro top using -inter flag (gro has
hydrogens, pdb does not)
3) use gro as input > take pdb output (pdb has hydrogens)

Thanks

Prasenjit Kumar Mukherjee
Graduate Student
Department of Medicinal Chemistry
School of Pharmacy
University of Mississippi
USA

Cell   - 662 380 0146
Office - 662 915 1286