[gmx-users] equilibration

Justin Lemkul jalemkul at vt.edu
Mon Jul 17 15:38:38 CEST 2017

On 7/14/17 7:43 AM, ‪farial tavakoli‬ ‪ wrote:
> Hi justin
>   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 

Parametrization by analogy is only a starting point.  In some cases it is 
straightforward and works well.  In others, it requires more effort.

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

Wrong bond?  How so?  Also, there are no bonds in coordinate files; if you're 
visualizing the coordinates and something funny shows up, that's a problem with 
the viewing program, not the topology itself.

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?

Sorry, I do not have time to check your work here.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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