farial.tavakoli at ymail.com
Fri Jul 14 13:54:05 CEST 2017
Thank you for reply and sorry for sending in another email, because when i wanted to reply, it was rejected.Actually, since i am a new gromacs user, i used all .mdp files ( em.mdp, nvt.mdp,...) in protein-ligand complex ( lysosym 4 ) tuturial in gromacs. And did all the steps and issued all commands that said in this tuturial . I also generated my ligand topology by PRODRG and edited the charges and charge groups . To edit atome charge, according to aminoacids.rtp file, i considered what my atomes are bonded to , in order to best give their charge. Then , regarding to the article : Practical considerations for building GROMOS-compatible small-molecule topologiesEditted the charge groups , but i think , maybe i was wrong in specifying charg groups. In addition, i noticed that there was a wrong bond in the gromacs topology ang gromacs cordinate files, so i corrected them but i dont know if i did right? These are all that i did. I dont know more about generating ligand topology but informatin that said in this tuturial. If you let me, send my ligand topology file to you?
With best regardsFarial
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