Re: [gmx-users] DMSO

[Mark Abraham]

Hi,

First, have you got your system working with just protein and water? And
just Protein, water and DMSO?

Mark

On Wed, Dec 21, 2016 at 3:08 AM Hoda Alibiglou 
wrote:

> Hello
>
> I am simulating a protein in mixture of water and DMSO, I madE the box
> including water and DMSO and my protein, now I should add ions by this
> command,
>
>
> gmx grompp -f ions.mdp -c dmso_D170W_solv.gro -p topol.top -o ions.tpr
>
> but, each time I get an error because the number of atoms in my
> topology file and
>
> dmso_D170W_solv.gro, are not equal, so I add in topology file SOL  and
> DMSO molecules number manually, now my error is that DMSO is unknown,
> also I used some references and according them I choosed gromos96
> forcefield for DMSO-WATER MIXTURE.
>
> may I ask you please to help me ?
>
> Best regards,
>
> Hoda
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Re: [gmx-users] DMSO

[tasneem kausar]

Check the total number of atoms in DMSO molecule.
after grompp you got an error of non-matching atom in gro and top file.
Subtract the number of molecule of top  file from molecule of gro file.
Divide the subtracted number with coordinates of DMSO. This gives the
number of DMSO molecule. Add this number to the top file.

Hope this will help

On Tue, Dec 20, 2016 at 9:38 PM, Hoda Alibiglou 
wrote:

> Hello
>
> I am simulating a protein in mixture of water and DMSO, I madE the box
> including water and DMSO and my protein, now I should add ions by this
> command,
>
>
> gmx grompp -f ions.mdp -c dmso_D170W_solv.gro -p topol.top -o ions.tpr
>
> but, each time I get an error because the number of atoms in my
> topology file and
>
> dmso_D170W_solv.gro, are not equal, so I add in topology file SOL  and
> DMSO molecules number manually, now my error is that DMSO is unknown,
> also I used some references and according them I choosed gromos96
> forcefield for DMSO-WATER MIXTURE.
>
> may I ask you please to help me ?
>
> Best regards,
>
> Hoda
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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> * For (un)subscribe requests visit
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[gmx-users] DMSO

[Hoda Alibiglou]

Hello

I am simulating a protein in mixture of water and DMSO, I madE the box
including water and DMSO and my protein, now I should add ions by this
command,


gmx grompp -f ions.mdp -c dmso_D170W_solv.gro -p topol.top -o ions.tpr

but, each time I get an error because the number of atoms in my
topology file and

dmso_D170W_solv.gro, are not equal, so I add in topology file SOL  and
DMSO molecules number manually, now my error is that DMSO is unknown,
also I used some references and according them I choosed gromos96
forcefield for DMSO-WATER MIXTURE.

may I ask you please to help me ?

Best regards,

Hoda
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