On 7/6/13 4:17 PM, Mark Abraham wrote:
On Sat, Jul 6, 2013 at 4:30 PM, Albert <mailmd2...@gmail.com> wrote:
On 07/06/2013 12:14 PM, Mark Abraham wrote:
My bad. Use
warning_note(wi, "Debugging");
thanks a lot Mark. I've obtained some informations now:
That's a completely different output. I think both your executables
are broken, somehow. Clean the build and install trees and try again
:-)
Mark
Identified residue MET1 as a starting terminus.
Warning: Residue RETK296 in chain has different type (Other) from starting
residue MET1 (Protein).
Warning: Residue THR297 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue SER298 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue ALA299 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue VAL300 in chain has different type (Protein) from starting
residue MET1 (Protein).
More than 5 unidentified residues at end of chain - disabling further
warnings.
Identified residue ALA295 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
Fatal error:
Residue 1 named LEU of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.
This problem can be solved by remembering to complete step 5 of
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field.
As Mark notes, though, this issue is entirely separate from your initial
problem.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Associate
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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