[gmx-users] Model of water
shima_arasteh2001 at yahoo.com
Sat Oct 6 16:52:00 CEST 2012
# grep -c P popc-solv.gro
What should I do with this number?
----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>
Sent: Saturday, October 6, 2012 6:17 PM
Subject: Re: [gmx-users] Model of water
On 10/6/12 10:45 AM, Shima Arasteh wrote:
> Yes, the system is only POPC and water.
Then it should be very easy to count how many molecules are in the system using
grep. Your topology specifies a lot more atoms than the coordinate file has.
The number of water molecules appears right, which leaves only the number of
POPC as the problem.
> ----- Original Message -----
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>
> 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:
>> 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
>> [ 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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