[gmx-users] Prot_prep_query

Hello Andrea, Thanks for your reply. Actually I am not doing a NMR constraint based refinement of the structure. Its a NMR derived ligand-protein complex submitted in the pdb. I want to prepare the complex using the tutorial. In the tutorial they have a crystal structure without hydrogens.

[gmx-users] Prot_prep_query

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