[gmx-users] adding mix solvent

Masumeh Asman asman.ma at gmail.com
Tue Sep 25 11:12:06 CEST 2012

On Tue, Sep 25, 2012 at 11:57 AM, Nur Syafiqah Abdul Ghani <
pqah123 at gmail.com> wrote:

> Dear All,
> I already produce my co-solvent topology file also with gro file.
> Next step is i need to put the co-solvent first before i enter the
> water molecule inside my box and mix them with the protein.
> But right now i had a problem during put the co-solvent part.
> I used this command : genbox -cp protein_box.gro -ci solv.gro -p
> control.top -o protein_solv.gro
> but then there was no any molecule of my co-solvent inside the box
> with the protein.
> Then i know i must have the itp file to include in the control topology.
> But what i can do with the topology of the co-solvent?What is the
> relationship between co-solvent.gro and
> co-solvent.top which i  might can used both of them in my GROMACS
> simulation?
> Four your infomation i used antechamber to produced my co-solvent topology.
> Any advises from the pro one?
> Thanks in advance!
> --
> Best Regards,
> Nur Syafiqah Abdul Ghani,
> Theoretical and Computational Chemistry Laboratory,
> Department of Chemistry,
> Faculty of Science,
> Universiti Putra Malaysia,
> 43400 Serdang,
> Selangor.
> 013-7188131
> alternative email : syafiqahabdulghani at gmail.com
> --
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Dear user
you need to determine the number of co-solvent molecule in genbox command
with -nmol option.


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