[gmx-users] Problem with pdb2gmx when used with OPLS and TIP4P

Manik Mayur manik.mayur at gmail.com
Wed May 13 22:36:55 CEST 2009 

On Thu, May 14, 2009 at 1:56 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Manik Mayur wrote:
>
>> On Thu, May 14, 2009 at 1:32 AM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    Manik Mayur wrote:
>>
>>        Hi Users,
>>
>>        I constructed a .pdb file for TIP4P water model which I tried to
>>        convert to .gro using pdb2gmx using:
>>
>>        $ pdb2gmx -f Sim1.pdb -o Sim1.gro -water tip4p
>>
>>
>>    There is no need to use pdb2gmx.
>>
>>    If you just need a TIP4P solvent box, one exists in the /share/top
>>    subdirectory of your Gromacs installation (tip4p.gro).
>>
>>
>> Thanks for the reply. I needed to use pdb2gmx as it automatically checks
>> for errors in the configuration file. Moreover apart from water, my system
>> has silicon walls enclosing water.
>>
>>
> OK, then that makes more sense.
>
>     If you want to use your configuration, use editconf to convert it to
>>    .gro and #include "tip4p.itp" in your topology (which you can write
>>    by hand for a simple water system), or leave it as .pdb; Gromacs can
>>    use many different file formats for structures.
>>
>>
>> yes, editconf will convert it to .gro but I was wondering why pdb2gmx is
>> behaving in such unexpected manner?
>>
>>
>>        with the choice of forcefield as 5 (OPLS-AA/L all-atom force
>>        field). After conversion I found that the position of HW3(MW),
>>        the dummy atom is not the same relative to OW, what I kept in
>>        the .pdb file. Even during the conversion pdb2gmx gave warnings
>>        as "Warning: Long Bond (1773-1776 =....".
>>
>>
>>    What values does it find? (... does not help)
>>
>>
>> e.g.
>> Warning: Long Bond (8637-8640 = 8.73449 nm)
>>  .. and so on for many more pairs (all ~8 nm)
>>
>>    Interestingly, if one runs pdb2gmx on the existing tip4p.gro that
>>    comes pre-installed, the program reports "Short bond" warnings.
>>
>>
>>        My .pdb file goes like this:
>>        ............
>>        ATOM   1773  OW  SOL   108      45.944  29.409  58.762  1.00  0.00
>>        ATOM   1774  HW1 SOL   108      46.530  29.409  59.519  1.00  0.00
>>        ATOM   1775  HW2 SOL   108      46.530  29.409  58.005  1.00  0.00
>>        ATOM   1776  HW3  SOL   108      46.094  29.409  58.762  1.00  0.00
>>        ............
>>        note that the OW - HW3 is 0.15 angs as it should be.
>>
>>
> The above is example is incorrect.  You have an extra space between HW3 and
> SOL, which (when I run pdb2gmx on it), generates the long bond warnings.
>  Check your .pdb file format and try again.
>

Indeed the format was the issue, thanks for the help.

-Justin
>
>         So why is pdb2gmx recalculating the co-ordinates of HW3? How is
>>        the OW-HW3 bond is getting stretched? Also, what should be the
>>        correct procedure for the conversion?
>>
>>
>>    The residue name "SOL" is interpreted as "HOH," or a three-point
>>    water molecule.  OPLS calls tip4p HO4 (per the .rtp file).  This
>>    could be a potential source of error.
>>
>>
>> with "-water tip4p" in pdb2gmx, SOL is interpreted as HO4, the default one
>> however is HOH.
>>
>> Thanks,
>>
>>    -Justin
>>
>>        Thanks,
>>
>>        Manik Mayur
>>        Graduate student
>>        Microfluidics Lab
>>        Dept. of Mechanical Engg.
>>        IIT Kharagpur
>>        INDIA
>>
>>
>>
>>  ------------------------------------------------------------------------
>>
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>>
>>    --    ========================================
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
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>>
>>
>> ------------------------------------------------------------------------
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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