Re: [AMBER] query

From: <sanjaykumar.imtech.res.in>
Date: Tue, 07 Apr 2015 16:01:16 +0530

 

Hello AMBER users

Thanks for reply.

I am new for AMBER. I have to do MD simulation of a protein having Fe
(2+). So first I am doing AMBER tutorial A1 "SIMULATING A SOLVATED
PROTEIN THAT CONTAINS NON-STANDARD RESIDUES". I did all the steps
required for generation of topology file for protein contacting Cu but I
now am stuck at stage 4, how to generate frcmod file (plc.frcmod) for
plastocyanine. What pdb file I should consider for generation of frcmod
file (plc.frcmod)? Is this contain Cu and its coordinated protein
residues? I want to know how author of above tutorial made this frcmod
file for plastocyanine.

Regards

Sanjay

On 2015-04-07 11:39, FyD wrote:

> Hi,
>
>> We have a protein which contain Iron (Fe2+, co-ordinated to Cys, His, His) and we are simulating this protein along with iron according to "AMBER TUTORIAL A1". Can you please tell us how to create a frcmod file with the changes specific to this project. Do we need to use some software, if so then please specify.
>
> See http://ambermd.org/formats.html [1]
> http://q4md-forcefieldtools.org/REDServer-Development/RED-Server-demo1.php [2]
> & its test case:
> http://q4md-forcefieldtools.org/REDServer-Development/popup/poptestcase.php [3]
> and frcmod file:
> http://q4md-forcefieldtools.org/REDServer-Development/Demo2-Files/frcmod.user [4]
>
> You could use PyRED at R.E.D. Server Dev. at
> http://q4md-forcefieldtools.org/REDServer-Development/ [5]
> frcmod files, LEaP script and force field libraries are generated
> from the PDB input files...
>
> See tutorials: http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php [6]
> and in particular
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo1.pdf [7]
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo21.pdf [8]
>
> regards, Francois
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber [9]

 

Links:
------
[1] http://ambermd.org/formats.html
[2]
http://q4md-forcefieldtools.org/REDServer-Development/RED-Server-demo1.php
[3]
http://q4md-forcefieldtools.org/REDServer-Development/popup/poptestcase.php
[4]
http://q4md-forcefieldtools.org/REDServer-Development/Demo2-Files/frcmod.user
[5] http://q4md-forcefieldtools.org/REDServer-Development/
[6] http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
[7] http://q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo1.pdf
[8] http://q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo21.pdf
[9] http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Apr 07 2015 - 04:00:02 PDT