[gmx-users] topology making by ATB/PRODRG

Justin Lemkul jalemkul at vt.edu
Tue Sep 1 13:33:10 CEST 2015

On 9/1/15 1:48 AM, elham tazikeh wrote:
> Dear GMX users
> i d simulated a drug on a protein and in *ions.tpr* production process, i
> ve got below error:
> *Fatal error:number of coordinates in coordinate file (sol.gro,
> 29108)             does not match topology (topol.top, 29116)*
> i know ATB server is useful for molecules at most 40 atoms and my ligand
> has 41 atoms,
> * is there any version of ATB  can support of upper 40 atoms in the
> ligand???*
> Now, i cant resolve my error....
> i know the meaning of this error , but for topology making of my ligand,
>   i used of ATB server and in ATB (*existing molecule section*)  , my
> molecule has *8Hydrogen* fewer than the main structure (*total charge
> was=zero*)

Because GROMOS force fields are united atom.

> i added Hydrogen atoms to my ligand by *cmd* program and *submit* my ligand
> to ATB server again for getting *lig.itp* correctly, but in ATB server, 3
> files have been seen that all of them had non zero total charges (-1)
> for this reason , i used of the topology file that existed in ATB server
> Even by using PRODRG server, i ve got a topology file that had non zero
> charges and COOH group assumed as COO- and 1H has been ignored...
> and in PRODRG server , i ve got 1H fewer than the main structure

Most servers assume physiological protonation.  If that's not what you 
want/need, then either you need to see if the server has options to change the 
default assumptions or you need to find another way to generate the topology.



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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