On Mon, 2014-02-10 at 17:07 +0000, Xu Zhou wrote:
> Dear Amber users,
>
> I want to do MD simulations for a complex after mutated 9 residues of it. But when I tried to use tleap to process this mutated complex, an error occurred: it exited from tleap directly when I tried to define ‘comp‘ showing:
>
> Loading PDB file: ./filename.pdb
> Illegal CONECT record in pdb file
> Illegal CONECT record in pdb file
> Illegal CONECT record in pdb file
> ......
>
> /cm/shared/apps/amber11/exe/tleap: line 17: 14295 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 $
tleap should not segfault like this in general. However, the error
message you received is likely helpful. Did you try deleting the CONECT
records at the bottom of the PDB file? In general, tleap does not need
them (one exception is disulfide bonds, in which case you will need to
manually add any disulfides).
My guess is that when you modified the PDB file (presumably by deleting
atoms and renaming residues), the atom numbers in the CONECT records
become incorrect. If tleap tried to bond two atoms that no longer
existed, a segfault is a very likely outcome if that attempt was not
protected (as seems to be the case).
HTH,
Jason
P.S. You say you used Amber 10, but your path says that this is Amber
11 (which could mean tleap from AmberTools 1.5 or tleap from AmberTools
1.4). It is always a good idea to use the latest version of AmberTools
to see if the issue has already been corrected, or at the very least
know exactly what version (and how many bug fixes) you are using.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 10 2014 - 09:30:03 PST
