Paymon Pirzadeh wrote:
OK! It worked! Thanks a lot again. But I have a final technical
question. After running grompp, it shows that my box has a net charge of
-0.99 . Do you think adding one Na+ and reducing the charge to +0.01 is
OK?! or even this 0.01 charge will cause me troubles?
Depending on the size of your system, rounding errors can occur. It is unusual
that the hundredths place would be showing this error. Usually you'd get
something like 0.99998 or something. Your water topology has a zero net charge;
is there something else in your system causing the -1 charge?
Adding a single Na+ to neutralize the charge may be appropriate, but that's up
to you based on what's in your system (something else may be broken, but I just
don't know).
-Justin
Sorry for tons of e-mails.
regards,
Payman
On Tue, 2009-08-25 at 14:38 -0400, Justin A. Lemkul wrote:
Paymon Pirzadeh wrote:
OK! That's fine. But what if I do not have permissions to make such
changes in the itp files? Also, isn't that the case that when you define
That's why I said copy the force field files into your local directory. Once
there, you can modify them.
sth for the second time, grompp will take the second one? Sorry for mass
of e-mail!
That is only true in the case of .mdp files.
-Justin
Payman
On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote:
Paymon Pirzadeh wrote:
I have done that already! I use my local copy to make my files. but how
can I get rid of this error? get into the oplsaanb.itp or include this
water model in the topology file before oplsaa.itp?
I don't understand what you're saying you've already done.
The problem is this: when grompp attempts to assemble the .tpr file, it reads
all of the information from the ffoplsaa*.itp files. It finds the directives
like [defaults], [atomtypes], etc in a pre-defined order. If, later, it finds a
duplicate of these directives, it complains. So when you #include your .itp
file with new [atomtypes], it generates the error because it is a duplicate
directive. You have to include the new atom types in ffoplsaanb.itp in the
[atomtypes] directive of this file. The rest of the topology shouldn't cause a
problem, just the [atomtypes] directive.
-Justin
Payman
On Tue, 2009-08-25 at 14:14 -0400, Justin A. Lemkul wrote:
Paymon Pirzadeh wrote:
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.
Make a copy in your local directory; grompp will use these before looking for
system-wide files. As a general rule, whenever developing new parameters or
adjusting files, do so locally before potentially messing yourself (or others) up :)
-Justin
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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--
========================================
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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--
========================================
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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