Nilesh Dhumal wrote:
Hello,
I have a .pdb file for water modecules.
When I run pdf2gmx command residure name "SOL" change "HOH". I am using
opls force field parameters.
Can you tell whats the problem.
There is no problem, per se. It appears that (in the latest version of the code
around line 1298 of pdb2gmx.c), pdb2gmx renames all water models "HOH" unless
they are TIP4P or TIP5P. Whether or not this is appropriate is another matter,
since all water .itp files (regardless of force field) appear to refer to water
as "SOL."
A lot of code changes have occurred in an effort to streamline topology
production. Please report back if this actually causes a problem later down the
line so it can be properly investigated before the release of version 4.5.
Also, make sure to always refer to the version you are using. Since development
has been very rapid lately, changes are occurring all the time.
-Justin
Here is my .pdb dfile
TITLE Protein in water
REMARK THIS IS A SIMULATION BOX
CRYST1 30.273 30.273 30.273 90.00 90.00 90.00 P 1 1
MODEL 1
ATOM 1 OW SOL 1 30.029 25.981 28.726 1.00 0.00
ATOM 2 HW1 SOL 1 30.271 25.107 28.304 1.00 0.00
ATOM 3 HW2 SOL 1 30.216 26.725 28.084 1.00 0.00
ATOM 4 OW SOL 2 14.532 6.560 16.036 1.00 0.00
ATOM 2591 HW1 SOL 864 5.172 6.310 18.849 1.00 0.00
ATOM 2592 HW2 SOL 864 6.771 6.137 19.128 1.00 0.00
TER
ENDMDL
NIlesh
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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://lists.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
