[gmx-users] Model of water

[Shima Arasteh]

The total atom of popc-solv.gro is 74672
grep HW gives me 48698
grep P gives me 1628

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!!

Please help me :(


Sincerely,
Shima


----- Original Message -----
From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
To: Justin Lemkul <jalemkul at vt.edu>; Discussion list for GROMACS users <gmx-users at gromacs.org>
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 <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>
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 <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
>

-- 
========================================

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

========================================