[gmx-users] Re: Query regarding Gromacs

[Justin A. Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor or help service, and you stand a much better chance of getting 
an answer by contacting the community.


I have never worked with a system like yours, so I don't know why you'd assume I 
have such a protocol.  In general, you should principally be concerned with 
deriving proper parameters for your copper ion and quinone:


http://www.gromacs.org/Documentation/How-tos/Parameterization

Please realize that parameterization is a very advanced topic (especially note 
the "Exotic Species" heading in the above page).


I have no idea what you mean by "the heteroatoms are getting converted to atoms" 
- is there some issue with PDB nomenclature (HETATM/ATOM)?  If so, there is no 
problem.


-Justin

charanya wrote:

Dear Mr. Justin A. Lemkul,

I am working on copper dependent amine oxidases which have quinone and copper 
cofactors. These are essential for the proper functioning of the enzyme.When I tried 
to minimize the complex, the heteroatoms are getting converted to atoms. I request you 
to kindly provide me with a protocol as to how to minimize these kind of proteins.


Thank you for your time and consideration.

Regards,
Charanya Muralidharan
Dept of Biochemistry, cell biology & Bioinformatics
Sankara Nethralaya
18 College Road
Chennai . 600 006
Phone: 044-28271616 Fax: 044-28254180
Please visit our web site:  www.supportsankaranethralaya.org

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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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[gmx-users] Re: Query regarding toplogy of Manganese ion in protein

[sonali dhindwal]

Hello,

I have a Manganese ion in my protein, for which i want to run MD simulation.
Could
you please help me to know how to generate topology file for Manganese
and which force field to use, as none of the force field in Gromacs
supports Mn ion.
Please Help
Regards

--
Sonali Dhindwal

--- On Wed, 24/3/10, sonali dhindwal  wrote:

From: sonali dhindwal 
Subject: Query regarding toplogy of Manganese ion in protein
To: gmx-users@gromacs.org
Date: Wednesday, 24 March, 2010, 5:35 PM

Hello,

I have protein in my protein, for which i want to run MD simulation.
Could you please help me to know how to generate topology file for Manganese 
and which force field to use, as none of the force field in Gromacs supports Mn 
ion.
Please Help
Regards

--
Sonali Dhindwal


   
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[gmx-users] RE: query about g_rdf and make_ndx

[Mauricio Sica]

> Dear All,
>  
>...I think I should generate an .ndx file with  all the atoms
> I need as well as the solvent molecules, but I have some basic problem
> in understanding the preparation of .ndx file, when I am executing the
> commnad make_ndx and select system, index file is being prepared, but
> there I can not specify groups , everytime  it is said that group is
> empty, I am doing some mistake , but can not detcet it, please help in
> this two matters.
>
>   regards
>   SANGEETA
>   

To make a group cosisting in residue 'X' and 'Y' and the group 
"SOL" (group 'Z' in the index file), at the  prompt of command

'make_ndx -f topol' 

you should type something like: 

'rX  &| rY &| Y'

And so on

Good luck





Dr. Mauricio P. Sica                    LEPP
Phone: (54011)4365-7100 ext. 169        Laboratorio de Expresión
R. Saenz Peña 354   y Plegado Proteico
(B1876BXF) Bernal, Buenos Aires Universidad de Quilmes
Argentina






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Re: [gmx-users] Re: query

[David van der Spoel]

chiradip chatterjee wrote:

HI friends
Thanks for your instant help. I got TFE
(trifluoroethanol) itp, pdb and gro files. Now I want
to disturb you again for a command. I have one TFE
molecule. I want to make a solvent box with 100 TFE
and 600 Water molecules. What are the commands to
translate this one TFE to 100TFE in a mixed solvent
box? [I found the water box filled with water in
share/tutor/water.]
Sorry to bother you, But it seems to be that you guys
are my teachers of GROMACS as I am just a 4 days old
baby in gromacs.
Chiradip



this is why you should run more tuturials and read mailing lists etc.
search for

genconf
genbox


--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] Re: query

[chiradip chatterjee]

HI friends
Thanks for your instant help. I got TFE
(trifluoroethanol) itp, pdb and gro files. Now I want
to disturb you again for a command. I have one TFE
molecule. I want to make a solvent box with 100 TFE
and 600 Water molecules. What are the commands to
translate this one TFE to 100TFE in a mixed solvent
box? [I found the water box filled with water in
share/tutor/water.]
Sorry to bother you, But it seems to be that you guys
are my teachers of GROMACS as I am just a 4 days old
baby in gromacs.
Chiradip

--- David van der Spoel <[EMAIL PROTECTED]> wrote:

> Paul van Maaren wrote:
> > On Sunday 12 November 2006 10:42, Tsjerk Wassenaar
> wrote:
> > 
> >> Probably someone will have a topology and a
> structure file for TFE
> >> lying around (not me). But TFE isn't the worst of
> molecules and since
> >> your new with Gromacs, I think it would be an
> excellent opportunity to
> >> get acquinted with the program and force fields
> by parameterizing it
> >> yourself. Find the paper of your favorite force
> field (choose one) and
> >> check how the parameterization of the building
> blocks / molecules was
> >> done. Take the same steps for TFE.
> >>
> >> Maybe this isn't the answer you'd hoped for, but
> think of the saying
> >> "give a man a fish and he can eat for a day;
> teach a man how to fish
> >> and..." :)
> > 
> > That's always a good approach, but for starters
> you might want to take a look 
> > at tfe.itp in the share/top directory.
> > 
> ... and check recent literature. IIRC there is a
> quite recent TFE model 
> for GROMOS-like force fields.
> 
> -- 
> David.
>

> David van der Spoel, PhD, Assoc. Prof., Molecular
> Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala
> University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:46 18 471 4205  fax: 46 18 511 755
> [EMAIL PROTECTED] [EMAIL PROTECTED]  
> http://folding.bmc.uu.se
>

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> 


Send instant messages to your online friends http://uk.messenger.yahoo.com 
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[gmx-users] Re: query TFE gro and itp file

[Mohan Boggara]

Dear Chiradip, May be try using PRODRG. Type PRODRG in google, and then draw your molecule, it will generate a topology and gro file for you. Mohan On 12/11/06, 
[EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
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Today's Topics:   1. Re: Re: How to generate GRO and TOP file for (Mark Abraham)   2. query (chiradip chatterjee)   3. Re: g_density for a micelle (Tsjerk Wassenaar)   4. Re: query (Tsjerk Wassenaar)
   5. Re: query (Paul van Maaren)--Message: 1Date: Sun, 12 Nov 2006 08:49:16 +1100From: Mark Abraham <
[EMAIL PROTECTED]>Subject: Re: [gmx-users] Re: How to generate GRO and TOP file forTo: Discussion list for GROMACS users Message-ID: <
[EMAIL PROTECTED]>Content-Type: text/plain; charset=ISO-8859-1; format=flowedMohan Boggara wrote:> However, to extend the gro file, we need to use the angle information
> and may be write a script.Molecule builders in various chemistry packages may be of help here. You  may need to use a text editor to change atom and residue names in theresulting structure files (presumably PDB) but it might be better than
writing your own script.> I don't know if this a good idea??A good idea is not to quote an entire daily digest when you intend onlyto refer to a small part of it. That digest gets sent to hundreds of
people through dozens of computers each... Well done for changing thesubject line to something relevant, though :-)Mark--Message: 2Date: Sun, 12 Nov 2006 04:45:29 + (GMT)
From: chiradip chatterjee <[EMAIL PROTECTED]>Subject: [gmx-users] queryTo: gmx-users@gromacs.orgMessage-ID: <
[EMAIL PROTECTED]>Content-Type: text/plain; charset=iso-8859-1Hi gromacs users,I am a new user in Gromacs. I need a help. I want to
make a solvent box with Trifluoroethanol(TFE) andwater. Could any one please supply me the *.gro and*.itp file for trifluoroethanol? I did not findthis(TFE) in the library file.thanks in advanceChiradip Chatterjee
Send instant messages to your online friends http://uk.messenger.yahoo.com--Message: 3Date: Sun, 12 Nov 2006 10:32:37 +0100
From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]>Subject: Re: [gmx-users] g_density for a micelleTo: "Discussion list for GROMACS users" <
gmx-users@gromacs.org>Message-ID: <[EMAIL PROTECTED]>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Chris,Aren't you looking for a radial distribution function (g_rdf)? Maybeyou'll have to change the code a bit to get exactly what you want, butI'd guess that g_rdf is closer to what you want. However, you do not
state what it is you want.., so it's merely a guess.Best,TsjerkOn 11/10/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]
> wrote:> Does anybody have a modified g_density for calculation from the center> of mass of a micelle?> Thanks.>> ___> gmx-users mailing list
gmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED].> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>--Tsjerk A. Wassenaar, Ph.D.post-docNMR, Utrecht University,Padualaan 8,3584 CH Utrecht, the NetherlandsP: +31-30-2539931F: +31-30-2537623--
Message: 4Date: Sun, 12 Nov 2006 10:42:42 +0100From: "Tsjerk Wassenaar" <[EMAIL PROTECTED]>Subject: Re: [gmx-users] queryTo: "Discussion list for GROMACS users" <
gmx-users@gromacs.org>Message-ID:<[EMAIL PROTECTED]
>Content-Type: text/plain; charset=ISO-8859-1; format=flowedHi Chiradip,Probably someone will have a topology and a structure file for TFElying around (not me). But TFE isn't the worst of molecules and since
your new with Gromacs, I think it would be an excellent opportunity toget acquinted with the program and force fields by parameterizing ityourself. Find the paper of your favorite force field (choose one) and
check how the parameterization of the building blocks / molecules wasdone. Take the same steps for TFE.Maybe this isn't the answer you'd hoped for, but think of the saying"give a man a fish and he can eat for a day; teach a man how to fish
and..." :)Cheers,TsjerkOn 11/12/06, chiradip chatterjee <[EMAIL PROTECTED]> wrote:> Hi gromacs users,> I am a new user in Gromacs. I need a help. I want to
> make a solvent box with Trifluoroethanol(TFE) and> water. Could any one please supply me the *.gro and> *.itp file for trifluoroethanol? I did not find> this(TFE) i

[gmx-users] Re: Query on Gromacs-CPMD QMMM Interface

[Pradip K Biswas]

Hi Sandeep,

To compile gmx-3.3.1_qmmm-1.3, the configure option --with-qmmm-cpmd does
not require CPMD to be compiled and installed beforehand. The preprocessor
flag just includes the calls for the interface to CPMD functions available
inside gmx-3.3.1_qmmm-1.3. You can compile gmx-3.3.1_qmmm-1.3
independently.

best,
pb.

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