OK!
here is the .itp file which I generated. I might upload it because it
has passed the initial tests.
; This is an itp file to describe water's six-site model by H. Nada and
J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413
(2003)
; This model is a combination of TIP4P and TIP5P. It has three LJ sites
and 3 Coulomb sites
; O-H bond length is 0.980A, HOH angle is 108.00degrees, LOL angle is
111.00 degrees, O-M and O-L are about 0.230A and 0.8892A respectively
[ defaults ]
; non-bondedtype combrule genpairs FudgeLJ
FudgeQQ N
1 2 NO
[ atomtypes ]
;name mass charge ptype c6 c12
OW 15.9994 0.0 A 0.3115 0.714845562
HW 1.00800 0.477 A 0.0673 0.11541
MW 0.000 -0.866 D 0.00 0.00
LW 0.00 -0.044 D 0.00 0.00
[ moleculetype ]
;molname nrexcl
SOL 2
[ atoms ]
; nr atomtype resnr residuename atom cgnr charge
1 OW 1 SOL OW 1 0.0
2 HW 1 SOL HW1 1 0.477
3 HW 1 SOL HW2 1 0.477
4 MW 1 SOL MW 1 -0.866
5 LW 1 SOL LP1 1 -0.044
6 LW 1 SOL LP2 1 -0.044
[ settles ]
; OW function doh dhh
1 1 0.0980 0.15856
[ dummies3 ]
; These set of parameters are for M site which can be easily calculated
using TIP4P calculations from tip4p.itp
; So, it will be described as dummy site 3: r(v)= r(i) + a*(r(i)-r(j)) +
b*(r(i)-r(k))
; const = |OH|/{|OH|*cos(HOH/2)} => Due to vector algebra a=b=const/2.
Remember that OM is in the same direction of OH bonds.
; Remember this site is in the same plane of OH bonds; so, its function
1
;
; site from function a b
4 1 2 3 1 0.199642536 0.199642536
; Now we define the position of L sites which can be obtained from
tip5p.itp
; So, it will be described as dummy site 3out: r(v) = r(i) +
a*(r(i)-r(j)) + b*(r(i)-r(k)) + c*(r(ij)Xr(ik))
; const1 = {|OL|*cos(LOL/2)}/{|OH|*cos(HOH/2)} => Due to vector algebra
|a|=|b|=const/2. since the lone pairs are in opposite direction of OH
bonds, a minus sign is added. This part is similar to M site.
; const2 = {|OL|*sin(LOL/2)}/{|OH|*|OH|*sin(HOH)} => The denominator is
the magnitude of vector product of OH bonds.
; This sites are tetrahedral sites; so, its function 4
;
; site from function a b
c
5 1 2 3 4 -0.437172388 -0.437172388
8.022961206
6 1 2 3 4 -0.437172388 -0.437172388
-8.022961206
[ exclusions ]
1 2 3 4 5 6
2 1 3 4 5 6
3 1 2 4 5 6
4 1 2 3 5 6
5 1 2 3 4 6
6 1 2 3 4 5
and here is the message I get from grompp:
Program grompp_d_mpi, VERSION 4.0.5
Source code file: topio.c, line: 415
Fatal error:
Syntax error - File sixsitewater.itp, line 12
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
-------------------------------------------------------
I believe the original files of GROMACS need admin permissions which I
do not have on the cluster that I am currently using and I am not sure
if that might not cause troubles for other users. So, I thought how I
can keep the changes local.
Payman
On Tue, 2009-08-25 at 13:53 -0400, Justin A. Lemkul wrote:
>
> 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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