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

[Justin A. Lemkul]

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.

-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

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