[AMBER] Regarding creating Mg2+ ions topology and parameter file

From: ROOPALI VERMA <roopaliverma7.gmail.com>
Date: Mon, 8 Jun 2015 16:01:53 +0530

Dear amber user,

I want to simulate a complex bound with ADP AND Mg2+ ions.For this i want
to create prmtop and crd files. i have created parameters file for ADP and
protein, but won't be able to create parameters file for Mg ions.i have
used antechamber but it shows following error:

* antechamber -i mgnew.pdb -fi pdb -o mg.mol2 -fo mol2 -c bcc -s 2 *

*Running: /home/drpunit/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC <http://ANTECHAMBER_AC.AC> -p gaffTotal number of
electrons: 0; net charge: 0Running: /home/drpunit/amber12/bin/sqm -O -i
sqm.in <http://sqm.in> -o sqm.outSegmentation fault (core dumped)Error:
cannot run "/home/drpunit/amber12/bin/sqm -O -i sqm.in <http://sqm.in> -o
sqm.out" of bcc() in charge.c properly, exit*
Please suggest me which protocol should i use to generaye the parameters
for Mg2+ ions.

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Received on Mon Jun 08 2015 - 04:00:02 PDT
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