Re: [AMBER] Amber14-GIST

From: Tom Kurtzman <simpleliquid.gmail.com>
Date: Thu, 21 Jun 2018 12:18:38 -0400

Hi Berkant, we've updated the tutorial but haven't yet pushed it to the
main website. We are in the process of doing so.

Please follow the instructions in the updated tutorial here:

https://www.dropbox.com/sh/6zr7y0modgeaxq6/AACb0CQi5XkdkUyAV65ijakza?dl=0

Tom





On Thu, Jun 21, 2018 at 4:42 AM, Berkant Düzgün <berkantkuzgun.gmail.com>
wrote:

> Hello,
> We were trying to use ambertools14 for GIST, there is a tutorial for it but
> it didn't work. We tried the same things in amber18 aswell. hthttp://
> ambermd.org/tutorials/advanced/tutorial25/section1.htm this is the
> tutorial
> we use.
> $AMBERHOME/bin/tleap
> > source leaprc.ff99SB
> > loadamberparams frcmod.ff99SB
> > loadoff Ca2.lib
> > prot = loadpdb ChainA_IONS_H.pdb
> > bond prot.7.SG <http://prot.7.sg/> prot.12.SG <http://prot.12.sg/>
> > bond prot.27.SG <http://prot.27.sg/> prot.43.SG <http://prot.43.sg/>
> > bond prot.156.SG <http://prot.156.sg/> prot.170.SG <http://prot.170.sg/>
> > bond prot.181.SG <http://prot.181.sg/> prot.209.SG <http://prot.209.sg/>
> > solvateBox prot TIP3PBOX 10
> > saveamberparm prot ChA_IONS_disul_TIP3P.top ChA_IONS_disul_TIP3P.inpcrd
> > quit
>
> thanks and have a nice day.
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 



-- 
************************************************
Tom Kurtzman, Ph.D.
Associate Professor
Department of Chemistry
Lehman College, CUNY
250 Bedford Park Blvd. West
Bronx, New York 10468
718-960-8832
http://www.lehman.edu/faculty/tkurtzman/
<http://www.lehman.edu/faculty/tkurtzman/index.html>
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Received on Thu Jun 21 2018 - 09:30:02 PDT
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