[gmx-users] topology making by ATB/PRODRG

elham tazikeh elham.tazikeh at gmail.com
Tue Sep 1 07:48:27 CEST 2015

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
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
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

i really appriciate for any help

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