Jack Shultz wrote:
Hi all,
I think I'm having a problem with the water models. Clearly ther are
differences in these tip3p models. I can rename the ffamber_tip3p
files to overwrite existing tip3p files. I don't want to do that
because I want the option of choosing the amber ones at run-time.
pdb2gmx does not accept a request for
-water ffamber_tip3p or -water amber_tip3p
The only way I have found to use the ffamber_tip3p is to manually modify the
topol.top after pdb2gmx (i.e., vi or sed), since the Amber force fields are not
standard within Gromacs. I suppose you could somehow modify the pdb2gmx code to
accept different options, but it's probably a lot easier to replace the text in
the post-pdb2gmx topology yourself.
-Justin
Are these the only options I can use?
-water enum spc Water model to use: with GROMOS we recommend
SPC, with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p or f3c
$ ls -l *tip3* *spc*
-rwx------+ 1 jshultz None 1377 Mar 17 11:22 Copy of tip3p.itp
-rwx------+ 1 jshultz None 106028 Feb 27 18:46 ffamber_tip3p.gro
-rwx------+ 1 jshultz None 638 Feb 27 18:46 ffamber_tip3p.itp
-rwx------+ 1 jshultz None 638 Feb 27 18:46 ffamber_tip3p_heavy.itp
-rwx------+ 1 jshultz None 36 Mar 17 11:21 flexspc.itp
-rwx------+ 1 jshultz None 37 Mar 17 11:22 flexspce.itp
-rwx------+ 1 jshultz None 1402 Mar 17 11:22 spc.itp
-rwx------+ 1 jshultz None 29266 Mar 24 07:40 spc216.gro
-rwx------+ 1 jshultz None 1142 Mar 17 11:22 spce.itp
-rwx------+ 1 jshultz None 106028 Feb 27 18:46 tip3p.gro
-rwx------+ 1 jshultz None 1377 Mar 24 07:40 tip3p.itp
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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
========================================
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