-------- Original Message --------
Subject: Re: [gmx-users] Model of water
Date: Sat, 06 Oct 2012 10:47:18 -0400
From: Justin Lemkul <jalem...@vt.edu>
To: Shima Arasteh <shima_arasteh2...@yahoo.com>
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.
-Justin
Sincerely,
Shima
----- Original Message -----
From: Justin Lemkul <jalem...@vt.edu>
To: Shima Arasteh <shima_arasteh2...@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
--
========================================
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
========================================
--
========================================
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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