[gmx-users] Model of water

Sat Oct 6 19:27:32 CEST 2012

Dear Justin,

I downloaded popc.pdb file from http://terpconnect.umd.edu/~jbklauda/research/download.html. This pdb file has water molecules. So I tried to run these commands and don't run genbox:
1.editconf -f popc.pdb -o popc.gro -c -d 1.0 -bt cubic
2.grompp -f em.mdp -c popc.gro -p topol.top -o em.tpr

I also added the SOL molecules manually as it is written at the end of the popc.pdb file downloaded.
But this fatal errors comes out:

Generated 21528 of the 21528 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 18355 of the 21528 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'POPC'
Excluding 2 bonded neighbours molecule type 'SOL'
Warning: atom name 2 in topol.top and popc.gro does not match (C12 - C11)
Warning: atom name 3 in topol.top and popc.gro does not match (C13 - C12)
Warning: atom name 4 in topol.top and popc.gro does not match (C14 - C13)
Warning: atom name 5 in topol.top and popc.gro does not match (C15 - C14)
Warning: atom name 6 in topol.top and popc.gro does not match (H12A - H11)
Warning: atom name 7 in topol.top and popc.gro does not match (H12B - H12)
Warning: atom name 8 in topol.top and popc.gro does not match (H13A - H21)
Warning: atom name 9 in topol.top and popc.gro does not match (H13B - H22)
Warning: atom name 10 in topol.top and popc.gro does not match (H13C - H23)
Warning: atom name 11 in topol.top and popc.gro does not match (H14A - H31)
Warning: atom name 12 in topol.top and popc.gro does not match (H14B - H32)
Warning: atom name 13 in topol.top and popc.gro does not match (H14C - H33)
Warning: atom name 14 in topol.top and popc.gro does not match (H15A - H41)
Warning: atom name 15 in topol.top and popc.gro does not match (H15B - H42)
Warning: atom name 16 in topol.top and popc.gro does not match (H15C - H43)
Warning: atom name 17 in topol.top and popc.gro does not match (C11 - C15)
Warning: atom name 18 in topol.top and popc.gro does not match (H11A - H51)
Warning: atom name 19 in topol.top and popc.gro does not match (H11B - H52)
Warning: atom name 20 in topol.top and popc.gro does not match (P - P1)
Warning: atom name 21 in topol.top and popc.gro does not match (O13 - O3)
(more than 20 non-matching atom names)

WARNING 1 [file topol.top, line 36]:
  8382 non-matching atom names
  atom names from topol.top will be used
  atom names from popc.gro will be ignored

Analysing residue names:
There are:    72      Other residues
There are:  2242      Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Number of degrees of freedom in T-Coupling group rest is 42393.00
Largest charge group radii for Van der Waals: 0.040, 0.040 nm
Largest charge group radii for Coulomb:       0.079, 0.079 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 96x96x96, spacing 0.116 0.116 0.116
Estimate for the relative computational load of the PME mesh part: 0.59

NOTE 1 [file em.mdp]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing

This run will generate roughly 191 Mb of data

There was 1 note

There was 1 warning

-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/grompp.c, line: 1584

Fatal error:
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.

Would you please give me advice? Thanks for all your explanation.

Sincerely,
Shima

----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>
Cc: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Saturday, October 6, 2012 7:25 PM
Subject: Re: [gmx-users] Model of water

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 <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

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