[AMBER] Starting antechamber for preparing ligand molecule

From: Anasuya Dighe <anasuya.mbu.iisc.ernet.in>
Date: Tue, 17 Mar 2015 22:53:51 +0530 (IST)

Dear Amber Users,
 I am interested in starting the simulation on a protein ligand complex.

 The ligand in question is a peptide inhibitor called Pepstatin. This molecule
has the Isovaleric Acid (IVA) and Statin (STA) chemical moieties. These
chemical moieties are connected to each other by a series of amino acids,
namely VAL (Valine) and ALA (Alanine). I have the following questions.
 (1) How do I go about using antechamber for such a system so as to obtain
.frcmod and ultimately prmtop &inpcrd (from leap) ? Do I use only the IVA and
STA chemical moieties for the antechamber calculations ? Or do I use the entire
molecule for it?
 (2) When I try using such a molecule and use antechamber to obtain the mol2
format of the molecule, I am getting the following error :

command used : antechamber -i pepstatin_new.pdb -fi pdb -o pepstatin_new.mol2
-fo mol2 -c bcc -s 2

 Running: /home/amber/amber14/bin/sqm -O -i sqm.in -o sqm.out
 Error: cannot run "/opt/apps/amber/amber12/bin/sqm -O -i sqm.in -o sqm.out" of
bcc() in charge.c properly, exit

 Here is the end of the output file of sqm.out
 QMMM: System specified with odd number of electrons ( 215)
 QMMM: but odd spin ( 1). You most likely have the charge of
 QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run

 (3) How do I go about solving these issues ? I tried reading up related posts
about the same error on Amber mailing list.
 But I would really appreciate help especially since the ligand system I wish to
simulate is a little different.
 Please help.

 Anasuya Dighe,

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Received on Tue Mar 17 2015 - 10:30:02 PDT
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