[gmx-users] Model of water

[Shima Arasteh]

Yes, the system is only POPC and water. 



 
Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>
Cc: 
Sent: Saturday, October 6, 2012 6:07 PM
Subject: Re: [gmx-users] Model of water



On 10/6/12 10:32 AM, Shima Arasteh wrote:
> OK.
> I did as follow as I described, but there is an error:
> 1.editconf -f popc.pdb -o popc-newbox.gro -c -d 1.0 -bt cubic
> 2.genbox -cp popc-newbox.gro -cs spc216.gro -o popc-solv.gro -p topol.top
>
> Then added #include "charmm36.ff/tip3p.itp" to topol.top
>
> 3.grompp -f em.mdp -c popc-solv.gro -p topol.top -o em.tpr
> Fatal error:
> number of coordinates in coordinate file (popc-solv.gro, 74672)
>               does not match topology (topol.top, 104936)
> I checked the water molecules of popc-solv.gro by grep command ;
>
> # grep -c HW popc-solv.gro
> 48696
>
>
> [ molecules ]
> ; Compound        #mols
> POPC              238
> SOL             24348
>
>
>
> What is the problem? would you please help me? I think the SOL molecule are counted twice!!
>

You're off by a huge amount of atoms, so something is very wrong.  The water 
molecules do not appear to be the problem.  The number of HW/2 is equal to the 
number of SOL molecules.  Is the system only POPC in water?  No protein or any 
other components?

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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