[gmx-users] Re:Newbie: How to modify the topology file after adding ions?

[lloyd riggs]

Message: 6
Date: Wed, 7 Dec 2011 11:38:58 -0500
From: Jose Borreguero <borreguero at gmail.com>
Subject: Re: [gmx-users] Newbie: How to modify the topology file after
    adding    ions?
To: jalemkul at vt.edu, Discussion list for GROMACS users
    <gmx-users at gromacs.org>
Message-ID:
    <CAEee4gVtQGT8zrqC+261xNPTr1usqvEu0kytG-ALeK3mAmn+8A at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi Justin, thanks for your reply!

I appended '-p protein.top' to genion. File protein.top was automatically
updated by insertion of the following lines at the end of the file:
*[ molecules ]
; Compound        #mols
Protein_chain_A     1
SOL         7791
NA+         26
CL-         23*

My solvated PDB, protein-solvent.pdb contains lines like these:
ATOM  24543  NA  NA+  8043      50.712  66.452  12.341  1.00  0.00

Now when I run grommp, I get the error
*Fatal error:
No such moleculetype NA+*

I checked file gromos45a3.ff/ions.itp. The sodium is included in this
fashion:
*[ moleculetype ]
; molname   nrexcl
NA          1
[ atoms ]
; id    at type res nr  residu name at name  cg nr  charge   mass
1       NA+     1       NA          NA             1        22.9898*

It seems the naming convention of ions.itp is different than that of
protein.top and protein-solvent.pdb. I changed protein.top and
protein-solvent.pdb to match the naming of ions.itp. Then when I run grompp
I get the error:
*ERROR 1 [file protein.top, line 7228]:
  ERROR: One of the box lengths is smaller than twice the cut-off length.
  Increase the box size or decrease rlist.*
The puzzling thing is that line 7228 of protein.top is the last line of the
file, that is,
CL      23
So the error message is not much help :(

-Jose

On Wed, Dec 7, 2011 at 11:04 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Jose Borreguero wrote:
>
>> Dear Gromacs users,
>>
>> Im new to gromacs and I'm following a tutorial (http://nmr.chem.uu.nl/~**
>> tsjerk/course/molmod/ <http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/>).
>> Unfortunately, the tutorials doesn't say anything about how to update the
>> topology file after using 'genion' to replace a few water molecules with
>> ions.
>> I manually edited the topology file and updated the number of water
>> molecules and added the number of ions:
>>
>>
> Using the -p flag will make all the necessary changes automatically.
>
>
>  [ molecules ]
>> ; Compound        #mols
>> Protein_chain_A     1
>> SOL              7791
>> Na+              26
>> Cl-              23
>>
>> But then when I tried to preprocess the structure with grompp, I got an
>> error:
>>
>> Fatal error:
>> No such moleculetype Na+
>>
>>
> Assuming you're using a new version of Gromacs (4.5.x), the naming scheme
> has changed.  Check the ions.itp for the force field you've chosen to use
> to set proper names.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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End of gmx-users Digest, Vol 92, Issue 36
*****************************************

1) The box error means your box deminsions are missing somewhere, either in a CRYST symetry box at the top of the .pdb file, or at the bottomn in an .gro file.

2) WHy is there a * after the CL?

you can also manually name the ions whatever you want and include an additional .itp file with all the parameters.  In addition, if you further add ions, the naming has to be in the same order as the ions in the .pdb or .gro file, ie the file has inserted the ions after the waters in the file, including the CL ions in this order...then the .top file has to read...

CL 28
NA 28
CL 45
CA2 45....etc.

Gutten Tag 

Stephan Watkins
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