On 10/6/12 11:52 AM, Shima Arasteh wrote:
The total atom of popc-solv.gro is 74672
grep HW gives me 48698
Assuming you meant to type 48696 like you reported before, this means there are
24348 water molecules, since there are two HW atoms per water (HW1 and HW2). If
you grep for OW (since it is unique to each water molecule), you can confirm the
count.
grep P gives me 1628
I already said this grep was insufficiently precise and thus it is not possible
to connect this information with the topology.
Section of moleculetypes in top file is as
[ molecules ]
Compound #mols
POPC 238
SOL 24348
I am confused! Am I need to change the number of gro or top file? Actually I
can't make connection between gro and top, so the coordinate doesn't match
topology yet!!
You need to make the topology agree with the coordinate file. Do not make
manual adjustments to the .gro file. Sometimes it's better to start over and be
more careful. A mismatch between coordinates and topology always boils down to
errors in bookkeeping.
-Justin
Please help me :(
Sincerely,
Shima
----- Original Message -----
From: Shima Arasteh <[email protected]>
To: Justin Lemkul <[email protected]>; Discussion list for GROMACS users
<[email protected]>
Cc:
Sent: Saturday, October 6, 2012 6:22 PM
Subject: Re: [gmx-users] Model of water
# grep -c P popc-solv.gro
1628
What should I do with this number?
Sincerely,
Shima
----- Original Message -----
From: Justin Lemkul <[email protected]>
To: Shima Arasteh <[email protected]>
Cc:
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.
-Justin
Sincerely,
Shima
----- Original Message -----
From: Justin Lemkul <[email protected]>
To: Shima Arasteh <[email protected]>
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
========================================
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