[gmx-users] acetaminophen charges

[elham tazikeh]

Dear GMX usere

my problems is in the assigning the ligand charges in protein-ligand
simulation

(for instance :acetaminophen )

i acquired (*.itp ) file by PRODRG (after optimization by gaussian
software) and ATB server as below.

which one is appropriate to my MD simulation by gromaces:


*atom*

*By prodrg server*

*By ATB server*

CH3

0.013

-0.062

C

0.590

0.734

O

-0.493

-0.643

N

-0.716

-0.706

H

0.328

0.422

C

0.336

0.337

CR1

-0.150

-0.229

HC

0.171

0.176

CR1

-0.181

-0.286

HC

0.133

0.181

C

0.378

0.379

OA

-0.650

-0.590

H

0.405

0.445

CR1

-0.213

-0.286

HC

0.118

0.181

CR1

-0.181

-0.229

HC

0.124

0.176

in addition to, in ATB server, i saw this message in the page

(molid; 29980 or 26014):


Warning! This molecule contains non-standard atom types not included in the
standard GROMOS 53A6 and 54A7 forcefield. To use these atom types the
internal GROMACS parameter files must be updated. These can be downloaded
using the link below. Instructions on where to place (and how to use) the
files are provided in the README file included in the archive.


Note: my force field was; gromos53A6

what is the meaning?

Regards