Dear Amber Mailing Listers,
I am trying to create a modified residue to introduce in my peptide.
Specifically it is about a serine at the neutral C-terminus, that is I added
a proton to the terminal -COO^- group.
After having calculated charges with Gaussian03 (following the RESP procedure
of the "Tutorial A1: Setting up a DNA-Ligand System") and created the
library file for the residue (enclosed in this email, seh.lib) I tried to
upload it in the whole peptide but unfortunately I got a "segmentation fault".
Below the series of commands I used:
:~>tleap
>source leaprc.ff99SBildn
>set default PBradii mbondi2
>loadOff seh.lib
>peptide = loadPdb peptide.pdb
$AMBERHOME/bin/tleap: line 8: 5540 Segmentation fault
$AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep
-I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm
-I$AMBERHOME/dat/leap/cmd $*
Any hint would be really appreciated.
Best regards,
--
Dr Massimiliano Porrini
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
E-mails : M.Porrini.ed.ac.uk
mozz76.gmail.com
maxp.iesl.forth.gr
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Received on Mon Aug 01 2011 - 09:30:03 PDT
