[gmx-users] Problem with pdb2gmx when used with OPLS and TIP4P
Justin A. Lemkul
jalemkul at vt.edu
Wed May 13 22:02:48 CEST 2009
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
> 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
> Manik Mayur
> Graduate student
> Microfluidics Lab
> Dept. of Mechanical Engg.
> IIT Kharagpur
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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