Paymon Pirzadeh wrote:
Hello,
Just a reminder that I had troubled with combination rules between my
water model and GROMACS forcefields. I fixed the problem by adjusting my
water model's parameters. BUT, now, I specified the new parameters in
my .itp file under [ atomtype ] category and grompp makes errors out of
the orders. Now I am using OPLSaa. I suspect again the problem comes
from the presence of the second [atomtype ]. How can I keep my new
parameters and use them in my water model's itp file? Or should I change
these parameters in the OPLSaa.itp file?
You can't have a second [atomtypes] directive. You can add new parameters to
ffoplsaanb.itp to account for the atom types you are implementing, though.
If you want anything more specific, you'll probably have to provide the topology
file you're working with, as well as any actual error messages you're seeing.
-Justin
Regards,
Payman
On Wed, 2009-08-19 at 10:20 +1000, Mark Abraham wrote:
Paymon Pirzadeh wrote:
I checked all the force-fields available in the GROAMCS. None of them
have the #2 combination rule which matches my water model! Any
alternatives (rather than changing my water model)?
A water model that isn't compatible with the model of the solutes isn't
of any value, so it looks like you have put the cart before the horse.
Mark
On Tue, 2009-08-18 at 18:52 -0400, Justin A. Lemkul wrote:
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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