Paymon Pirzadeh wrote:
That was very helpful! But I realized a problem. The OPLSaa uses the
combination rule #3 in [ defaults ] while my water model uses #2. Now if
I comment out my water model's combination, I am not sure what I am
going to face! Any comments?
Then I would say that your water model's combination rule is inconsistent with
the method of nonbonded calculations in OPLS. It appears that the only
difference between combination rules 2 and 3 comes when a specific interaction
is not defined in the [nonbond_params] section. The specifics of these
combination rules are given in manual section 5.3.3.
-Justin
Payman
On Tue, 2009-08-18 at 18:19 -0400, Justin A. Lemkul wrote:
Paymon Pirzadeh wrote:
Well,
I changed the topology file of the system and manually typed the .itp of
my own water model. Just a reminder that I have used my own water
model's .itp file successfully in pure water systems. This .itp file
starts from [ defaults ] and contains all information needed. But when
it comes to grompp, the following error appears:
Program grompp_d_mpi, VERSION 4.0.5
Source code file: topio.c, line: 415
Fatal error:
Syntax error - File sixsitewater.itp, line 6
Last line read:
'[ defaults ]'
Invalid order for directive defaults
The only time that [defaults] should appear is in the force field that you are
calling (i.e., ffoplsaa.itp):
http://oldwiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults
-Justin
I am trying to use this water model with OPLSaa. what kind of directive
am I missing?
Payman
On Tue, 2009-08-18 at 16:05 -0400, Justin A. Lemkul wrote:
Paymon Pirzadeh wrote:
Hello,
I am trying to use a different water model for my proteins (using oplsaa
force field). I use the .itp file which I developed, but pdb2gmx does
not accept it. I am a bit confused on how I can make my water model work
with OPLSaa. Based on what I saw from spc.itp or other samples, do I
need to change the names of my particles in my water .itp file by
including _FF_OPLS?
I don't know how pdb2gmx decides how to recognize water models; it may be
hard-coded. In any case, your atom types have to be consistent with OPLS
standards; as for whether or not you need the #ifdef _FF_OPLS in your .itp file,
you may not need it if OPLS is the only force field with which it will be used.
The #ifdef blocks just prevent a GROMOS system from trying to recognize OPLS, etc.
-Justin
Regards,
Payman
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--
========================================
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
========================================
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