[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 > outpu

Re: [gmx-users] Prot_prep_query

Hi Prasenjit, First, please don't include a whole digest into your reply :S What a scroll down. Did pdb2gmx say anything when not giving hydrogen atoms? It sounds weird that they were added in the .top but not in the .itp. Maybe first clean the directory, such that you only have the original .pd

[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. Sinc