Dear Saly
I attached for you the SW itp file: inside there is the
reference to the original paper.
You can find the SWM4 topology at the
http://oldwww.gromacs.org/pipermail/gmx-users/2006-August/023476.html
For SWM4-NDP I attach for you the topology that I created from the
reference paper.
Please check the parameter values with the ones reported in the original
paper...I am only a man and I usually make a lot of mistakes.
Concerning the force field I would like to advice you. You did not tell
me what you want to do with your water...
If you have to solvate something in water you have to be careful.
Common force field (oplsa, gaff etc.) are not parametrize for these kind
of water models that are quite recent.
For example, I know that there is some recent ion parametrization in
SWM4-NDP water ( J.Chem. Theory Comput. Lamoureux et. al., 2010)....
So I suggest you to check in literature how common force field behave
with these water models or to make some preliminary test...
All the best
Ivan
On 4/27/2011 10:08 PM, saly jackson wrote:
Hi Ivan
Please do not reply to whole digests with non-descriptive subject lines.
It confuses the archives, and alienates people from finding out the
topic of your interest, and thus being bothered to give you free help.
Please leave only the relevant discussion, and use a useful subject line.
In which force field can I find the polarizable water models you said
in section "b" of your reply
Have you done your own literature searching first? Then you'd already
know what force fields they might have been used with...
Mark
On 04/27/2011 02:08 PM, saly jackson wrote:
Hi Ivan
In which force field can I find the polarizable water models you said
in section "b" of your reply
Thanks alot
Regards
Saly
------------------------------
Message: 3
Date: Wed, 27 Apr 2011 12:14:42 +0200
From: Ivan Gladich <ivan.glad...@marge.uochb.cas.cz
<mailto:ivan.glad...@marge.uochb.cas.cz>>
Subject: Re: [gmx-users] POL3 water model
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <4db7ec92.7080...@marge.uochb.cas.cz
<mailto:4db7ec92.7080...@marge.uochb.cas.cz>>
Content-Type: text/plain; charset="iso-8859-1"
Dear Saly
from my little experience, POL3 water model is a point
polarizable
water model.
Point polarizable water models are not available in gromacs.
Gromacs uses shell model, i.e. charge attached on a spring to
mimic the
stretching of the electronic cloud.
So you have 3 solutions
a) You can take the POL3 model, look the polarizability of oxygen and
hydrogen atom and attach shells on oxygen and hydrogens atoms in
order
to reproduce the model for gromacs.
b) In Gromacs there are other polarizable water models using shell
(e.g.
SWM4-DP, SWM4-NDP, SW ), you could try with one of this...in my
opinion this is the best solution..;)
c) If you really need POL3 model, try with other molecular package
that
have point polarizable POL3 water (e.g. AMBER)
I hope this help
Ivan
On 04/27/2011 11:04 AM, saly jackson wrote:
> Hi all
>
> I want to simulate using GROMACS.Before I used LAMMPS but it has not
> polarizable water models. Therefore I want to use GROMACS.
>
> I need .itp and .mdp files of POL3 water model.
>
> Do you have the files.
>
> Would you please help me.
>
> Thanks alot for your time and attention
>
> Regards
>
> Saly
--
------
Ivan Gladich, Ph.D.
Postdoctoral Fellow
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
Czech Republic
Tel: +420775504164
e-mail: ivan.glad...@uochb.cas.cz <mailto:ivan.glad...@uochb.cas.cz>
web page:http://www.molecular.cz/~gladich/
<http://www.molecular.cz/%7Egladich/>
-----
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Message: 4
Date: Wed, 27 Apr 2011 14:22:20 +0430
From: mohsen ramezanpour <ramezanpour.moh...@gmail.com
<mailto:ramezanpour.moh...@gmail.com>>
Subject: Re: [gmx-users] Docking
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <banlktikk78dy35r97bnigoyswzvd4cu...@mail.gmail.com
<mailto:banlktikk78dy35r97bnigoyswzvd4cu...@mail.gmail.com>>
Content-Type: text/plain; charset="iso-8859-1"
Dear Mark
Thank you for your reply.yes,you are right.
Regarding question 2:
I have a pdf file from "Docking Server" for sertraline-SERT
example.Suppose
this is a good docked state.
In the other hand,I did what I explained in section 1 for
sertraline and
SERT.(by pymol and ...)
Now, I want to check if I have docked sertraline to SERT correctly
or not(
by comparing with Docking server's one)
How can I do that?
Do you have any suggestion for doing docking by gromacs? for
example pulling
code, MD , or SMD?
Thanks in advance
On Wed, Apr 27, 2011 at 1:48 PM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>>wrote:
> On 4/27/2011 7:05 PM, mohsen ramezanpour wrote:
>
>> Dear Users
>>
>> I read so many emails to mailing list, there were important
notes about
>> docking but I couldn't extract a general result.
>> Please let me know:
>>
>> 1-Can we dock a ligand to it's protein's binding pocket with
Pymol and
>> Gromacs as following?
>>
>> first:locating ligand outside and close to binding site
manually in pymol
>> and saving complex.pdb
>> second:doing all steps for generating complex.top and
complex.gro as
>> Enzyme-Drug tutorial
>> third:running md (with out any pull code and constraint),in the
other
>> words,full flexible system.
>>
>> I think drug can move freely and according to it's interaction with
>> binding site can be attracted by binding site.
>> reside for a distance time and then will come out of pocket.
>>
>> Am I right?
>>
>
> In principle, yes, but it is wildly unlikely that you have a
system that
> can bind and unbind reliably in the 100ns simulation range that
you might be
> able to afford to run, and if you did happen to have one, what
would you
> have learned?
>
>
> I know what discussed in mainling list about deffinition of
"Docking".
>>
>>
>> 2-I have some docked files by "Docking Server " for some of my
>> drug-protein's complexes.
>> now,I want to obtain them by doing MD in the above proccess.if
I was
>> successful then try to do that for other drugs which I don't
have any docked
>> pdb for them.
>>
>> How can I fit a trajectory with a typical pdb file?
>>
>
> I don't understand what you are asking.
>
> Mark
>
>
>
> --
> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
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> Please search the archive at
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End of gmx-users Digest, Vol 84, Issue 213
******************************************
--
------
Ivan Gladich, Ph.D.
Postdoctoral Fellow
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
Czech Republic
Tel: +420775504164
e-mail: ivan.glad...@uochb.cas.cz
web page:http://www.molecular.cz/~gladich/
-----
;
; Topology file for SW
;
; Paul van Maaren and David van der Spoel
; Molecular Dynamics Simulations of Water with Novel Shell Model Potentials
; J. Phys. Chem. B. 105 (2618-2626), 2001
;
; Force constants for the shell are given by:
;
; k = qs^2/(4 pi eps0 alpha)
; However, in the current version of the itp file and software (3.2+)
; force constants are computed in mdrun, and the input is the
; polarizability in nm^3.
;
; Some data: mu (water) = 1.8546 D ( 0.0386116 e nm)
; 1/(4 pi eps0 alpha) = 94513.94
;
; Alpha-X = 1.415 kx = 608069
; Alpha-Y = 1.528 ky = 563101
; Alpha-Z = 1.468 kz = 586116
;
; Alpha = 1.470 k = 585318
;
; Bonding parameters from (but without cubic term):
; D. M. Ferguson:
; Parametrization and Evaluation of a Flexible Water Model
; J. Comp. Chem. 16(4), 501-511 (1995)
;
; Possible defines that you can put in your topol.top:
; -DANISOTROPIC Select anisotropic polarizibility (isotropic is default).
; -DRIGID Rigid model (flexible is default)
; -DPOSRES Position restrain oxygen atoms
;
[ defaults ]
LJ Geometric
[ atomtypes ]
;name mass charge ptype c6 c12
WO 15.99940 0.0 A 0.0 0.0
WH 1.00800 0.0 A 0.0 0.0
WS 0.0 0.0 S 0.0 0.0
WD 0.0 0.0 D 0.0 0.0
[ nonbond_params ]
#ifdef RIGID
#ifdef ANISOTROPIC
WH WH 1 4.0e-5 4.0e-8
WS WO 1 1.0e-6 1.0e-12
WS WH 1 4.0e-5 2.766e-08
WO WO 1 2.0e-3 1.174e-06
#else
WH WH 1 4.0e-5 4.0e-8
WS WO 1 1.0e-6 1.0e-12
WS WH 1 4.0e-5 2.769e-08
WO WO 1 2.0e-3 1.176e-06
#endif
#else
#ifdef ANISOTROPIC
WH WH 1 4.0e-5 4.0e-8
WS WO 1 1.0e-6 1.0e-12
WS WH 1 4.0e-5 2.910e-08
WO WO 1 2.0e-3 1.189e-06
#else
WH WH 1 4.0e-5 4.0e-8
WS WO 1 1.0e-6 1.0e-12
WS WH 1 4.0e-5 2.937e-08
WO WO 1 2.0e-3 1.187e-06
#endif
#endif
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; This is a the 'classical YAW' model, in which we do have the dummy.
;; The shell is attached to the dummy, in this case the gas-phase
;; quadrupole is correct. Water_pol routine can be used for this
;; model. This has four interaction sites.
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
[ moleculetype ]
; molname nrexcl
SW 2
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 WO 1 SM2 OW1 1 1.24588
2 WH 1 SM2 HW2 1 0.62134
3 WH 1 SM2 HW3 1 0.62134
4 WD 1 SM2 DW 1 0.0
5 WS 1 SM2 SW 1 -2.48856
#ifdef ANISOTROPIC
[ water_polarization ]
; See notes above. Alphas in nm^3 (See ref. above)
; O H H D S funct al_x al_y al_z rOH rHH rOD
1 2 3 4 5 1 0.001415 0.001528 0.001468 0.09572 0.15139 0.0137408
#else
[ polarization ]
; See notes above. alpha (nm^3)
4 5 1 0.00147
#endif
#ifdef RIGID
[ settles ]
; i funct dOH dHH
1 1 0.09572 0.15139
#else
[ bonds ]
1 2 1 0.09572 458148.
1 3 1 0.09572 458148.
[ angles ]
; i j k
2 1 3 1 104.52 417.6
#endif
[ dummies3 ]
; The position of the dummies is computed as follows:
;
; O
;
; D
;
; H H
;
; 2 * b = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]
; 0.0137408 nm / [ cos (104.52 / 2 deg) * 0.09572 nm ]
; 0.01557 nm
; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-X1)
;
; Dummy from funct a b
4 1 2 3 1 0.117265878 0.117265878
[ exclusions ]
; iatom excluded from interaction with i
1 2 3 4 5
2 1 3 4 5
3 1 2 4 5
4 1 2 3 5
5 1 2 3 4
#ifdef POSRES
; Restrain the oxygen...
[ position_restraints ]
; iatom type fx fy fz
1 1 100 100 100
#endif
;Ivan Gladich, Prague 26/02/2011
; Topology file for SWM4-NDP obtained from
;
; G. Lamoureux, A. D. MacKerell, Jr., B. Roux et. al.
; A polarizable model of water for molecular dynamics simulations of
biomoleculesbased on classical Drude oscillators
; Chem. Phys. Lett.,418,245-249, 2005
;
[ defaults ]
;nbfunc (1=LJ,2=Buck)
1 2
[ atomtypes ]
;name mass charge ptype sigma epsilon
WO 15.99940 0.0 A 0.318395 0.88257296
WH 1.00800 0.0 A 0.0 0.0
WS 0.0 0.0 S 0.0 0.0
WD 0.0 0.0 D 0.0 0.0
[ moleculetype ]
; molname nrexcl
SW 2
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 WO 1 SM2 OW1 1 1.71636
2 WH 1 SM2 HW2 1 0.55733
3 WH 1 SM2 HW3 1 0.55733
4 WD 1 SM2 DW 1 -1.11466
5 WS 1 SM2 SW 1 -1.71636
[ polarization ]
; See notes above. alpha (nm^3)
;The drude particle is attached to the oxygen atom!!!!!
1 5 1 0.00097822
[ settles ]
; dHH = 0.15139 gives HOH agle equal to 104.52 degree
; i funct dOH dHH
1 1 0.09572 0.15139
;[ constraints ]
; i funct doh dhh
;1 2 1 0.09572
;1 3 1 0.09572
;3 2 1 0.15139
[ virtual_sites3 ]
; The position of the dummies is computed as follows:
;
; O
;
; D
;
; H H
; "a" and "b" are wieight
;the dummy 4 is in the plane of atom 1 2 3.
;Function 2 means that rd= rO+b(rOH1+arH1H2)/|rOH1+arH1H2|(see manual)
;so a=1/2 and b the distance from the oxygen atom
; Dummy from funct a b
4 1 2 3 2 0.5 0.024034
[ exclusions ]
; iatom excluded from interaction with i
1 2 3 4 5
2 1 3 4 5
3 1 2 4 5
4 1 2 3 5
5 1 2 3 4
[ system ]
Ice TIP5P-Ew T300
[ molecules ]
SW 1792
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