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

[Justin A. Lemkul]

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).

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.

> 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)

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.
> 
> 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.

-Justin

> Thanks,
> 
> Manik Mayur
> Graduate student
> Microfluidics Lab
> Dept. of Mechanical Engg.
> IIT Kharagpur
> INDIA
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

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

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