[gmx-users] Charge on drug

[tasneem kausar]

Dear All


I am using Acpype server to generate topology file of drug molecule to
perform protein drug MD simulation. Acpype have generated the itp file and
other necessary for MD simulations. I am doing MD on gromacs 5.1.4 software
using amber99sb force field. When I have done energy minimization some
unwanted bonds are formed in drug molecule. So the position restraint is
not able to execute. The problem is due to the unusual bond in drug atom.
When I used the itp file of PRODRG server position restraint goes
successfully. I have used the gromos54a7 ff. But there is problem with the
charge present on the atom that comes from PRODRG.

Please tell me how charge on the atom can be corrected in itp file of
PRODRG.  How the problem in energy minimization with the Acpype itp will be
resolved.

Thanks in Advance
With Regards
Tasneem