[gmx-users] Energy minimisation of solvated protein - Tutorial

[Tsjerk Wassenaar]

Hi Nayef,

Can you

- copy-paste the sequence of commands as you have typed them in (not
as you think you typed them in or as they're given in the tutorial)
- provide the output of 'tail 1qlz-water.gro'

Cheers,

Tsjerk

On Mon, Jun 21, 2010 at 9:49 PM, Nayef Daher <elthaher at ualberta.ca> wrote:
> Hi,
>
> I have the same problem as listed below back in February. I am using the
> latest gromacs version (4.0.7) and tried the solution below by entering
>
> genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro
>
> instead of making the output as pdb file. Yet the same result occurs with
> the same error message. One of the box lengths is smaller than twice the
> cut-off length.
>
> Please let me know what other options I can try.
>
> Thanks!
>
> nayef
> ------------------------------------------------------------------------------
> original message below
> ------------------------------------------------------------------------------
>
> Hi Anna,
>
> You should mention the version of Gromacs you're using. One of the
> versions did not write the box correctly to pdb files, which I think
> happened in your case. If you take as the solvation step
>
> genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro
>
> instead of writing output to 1qlz-water.pdb, I think you should be fine.
>
> The reason for writing a .pdb file is the easier visualization with a
> multitude of programs.
>
> Thanks for your interest in the tutorial.
>
> Cheers,
>
> Tsjerk
>
> On Fri, Feb 26, 2010 at 1:27 PM, Anna Duncan
> <anna.duncan at mrc-mbu.cam.ac.uk> wrote:
>>
>> Hi,
>>
>> I've been trying to go through the 'Introduction to Molecular Dynamics
>> Simulations and Analysis' tutorial written by Tsjerk Wassenaar, one of the
>> tutorials listed on the GROMACS website.
>>
>> I've got to the stage where I am performing energy minimisation on my
>> solvated protein but when I use grompp to create the .tpr file for mdrun,
>> I
>> get the error message:
>>
>> One of the box lengths is smaller than twice the cut-off length. Increase
>> the box size or decrease rlist
>>
>>
>> I am using the protein with pdb ID 1QLZ, one of the suggested structures
>> for
>> the tutorial and have so far carried out the following commands:
>>
>> % pdb2gmx -f 1qlz.pdb -o 1qlz.gro -p 1qlz.top -ignh
>> % grompp -f minim.mdp -c 1qlz.gro -p 1qlz.top -o 1qlz-EM-vacuum.tpr
>> % mdrun -v -deffnm 1qlz-EM-vacuum.tpr -c 1qlz-EM-vacuum.pdb
>> % editconf -f 1qlz-EM-vacuum.pdb -o 1qlz-PBC.gro -bt dodecahedron -d 1.0
>> % genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.pdb
>> % grompp -v -f minim.mdp -c 1qlz-water.pdb -p 1qlz.top -o 1qlz-water.tpr
>> % genion -s 1qlz-water.tpr -o 1qlz-solvated.pdb -conc 0.15 -neutral -pname
>> NA+ -nname CL-
>> % grompp -v -f minim_pbc.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o
>> 1qlz-EM-solvated.tpr
>>
>> after which I receive the error message.
>>
>> The minim_pbd.mdp file I use in the last grompp command is the same as
>> minim.mdp used in previous grompp commands (the latter file I downloaded
>> as
>> part of the tutorial) except that the line 'pbc = no' has been replaced by
>> 'pbc = xyz'.
>>
>> I have tried increasing the value of 'd' in the editconf command, to 2,3
>> and
>> even 8 but this doesn't make any difference.  (I have read that it is not
>> a
>> good idea to tamper with the cut-off values so have avoided doing that)
>>  The
>> box vector lengths when d = 1.0 are all 7.10051, and rvdw, rcoulomb = 1.0
>> in
>> mimim.mdp and minim_pbd.mdp, so I don't understand what is going wrong...
>>
>> Anna
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands