[AMBER] Amber14-GIST

From: Berkant Düzgün <berkantkuzgun.gmail.com>
Date: Thu, 21 Jun 2018 11:42:52 +0300

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.
> 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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Received on Thu Jun 21 2018 - 02:00:03 PDT
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