[AMBER] Antechamber and GTP

From: Fernando Martín García <fmgarcia.cbm.uam.es>
Date: Wed, 14 Nov 2012 11:56:42 +0100

 Dear Amber users,

 I'm trying to obtain my ligand prep and frcmod files of GTP following
 this tutorial:

        
 http://mmtsb.org/workshops/mmtsb-ctbp_workshop_2009/Tutorials/Antechamber_sustiva/antechamber.html

 But I have some problems with the first step: pdb to mol2, since I have
 next error

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

 Here is my command line:

        antechamber -i gtp.pdb -fi pdb -o gtp.mol2 -fo mol2 -c bcc -nc
 -4 -s 2

 I also tried without -nc -4, but with the same results.

 Is there any problem with sqm and gtp ligand for this calculation?

 Thank you.

 Best regards,

 Fernando 

-- 
 ==============================================
  Fernando Martín García
  Molecular Modelling Group - Lab 312.1
  Molecular Biology Center "Severo Ochoa"
  C/ NICOLáS CABRERA, 1.
  UAM University. Cantoblanco, 28049 Madrid. Spain.
  TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
  Web: http://fertoledo.wordpress.com/
 ==============================================
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Received on Wed Nov 14 2012 - 03:00:04 PST
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