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 [email protected]
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 [email protected].
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
========================================
_______________________________________________
gmx-users mailing list [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
