Dear All,
I have posted this question a few days ago, I still get the same error message even after changing the force field parameters to ff99SB.
I am following this tutorial to carry out free energy calculation of ligands binding to the receptor. (
http://ambermd.org/tutorials/advanced/tutorial24/)
While setting up MD simulations using this command file : http://ambermd.org/tutorials/advanced/tutorial24/files/setup_am1_3trj_MDs
For some of the ligands it is crashing instantly with this below mentioned error:
AMBER General Force Field for organic molecules (Version 1.8, Mar 2015)
Loading library: /home/local/soemya-loc/site_1_WT/leap/ZINC01532529/ZINC01532529_am1.lib
File: /home/local/soemya-loc/site_1_WT/CA.lib is not a valid database.
Loading PDB file: /home/local/soemya-loc/site_1_WT/leap/ZINC01532529/ZINC01532529_lig.pdb
Error: Atom .R<<1> 1>.A<C5 6> has force field coordination 4
but only 3 bonded neighbors.
The cause may be an incorrect atom type, and
the effect may be a crash very soon.
Error: Atom .R<<1> 1>.A<O1 7> has force field coordination 2
but only 1 bonded neighbors.
The cause may be an incorrect atom type, and
the effect may be a crash very soon.
/opt/amber16/bin/tleap: line 17: 19992 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 $*
The standard lib CA.lib shows is not valid for this (ZINC01532529 : this particular ligand is Methionine) ?
Please help me in this regard. I am not able to find the reason why this crashed.
Please refer to the attached file. (log file and command file to set MD)
Thanks
Regards
Sowmya
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Received on Mon Mar 27 2017 - 07:00:03 PDT
