Dear Javad,

Change SDMSO atomtype to SDmso in the ligand.itp file.

Best,

HHA

Simply delete "title" option from our mdp file. It is not used any more.

Position restraints: at some point you will wish the simulation box to represent reality as much as possible. In a lab of your colleague, are there any position restraints in a test tube with protein?

It is an artificial method which can be useful in the initial stages of molecular dynamics.

Dear javad,

If you use pdb2gmx, the -i option makes it write a posre.itp file for your non-hydrogen atoms.This is then included in the topology file using #include "posre.itp" section (as a restraint section).

best,

HHA

Thanks for your responses Michal Kolář and Hamed Haghshenas,

Yes, We have this position restrain in our collage's lab.

My big problems are topology and coordinate's files that PRODRG Server produce for my Ligand; In an initial stage when I want to insert my data to Grompp, This program starting to output errors.

In your opinion what's the wrong with my work? and am I insert my input files correct in the app?

Dear Javad,

Salam

Error type in Grompp depends on your input files.So, What is the exact error message?

Dear friend send me your input files I will consider it...

Best,

HHA

Salam Hamed Jan

I'm working with molecule containing sulfonamides groups , when I run grommp ,I'm wrong such as Group SDMSO is unknown. Do you think I should do?Is there a way to ensure the accuracy of atomic charges has changed there?

Dear Javad,

Change SDMSO atomtype to SDmso in the ligand.itp file.

Best,

HHA