Re: [AMBER] FEW- issues generating parameter files for MD

From: Sowmya Indrakumar <soemya.kemi.dtu.dk>
Date: Mon, 27 Mar 2017 15:18:40 +0000

Hi Andreas, Please find attached the PDB file and log file for one of the other ligand for which it failed as well. I look forward for your suggestions. Thanks Regards Sowmya ________________________________________ From: Andreas Tosstorff [andreas.tosstorff.cup.uni-muenchen.de] Sent: Monday, March 27, 2017 4:20 PM To: amber.ambermd.org Subject: Re: [AMBER] FEW- issues generating parameter files for MD Hi Sowmya, can you send us the pdb file of the ligand please? Also, have you considered using gaff2? Best, Andy On 03/27/2017 03:57 PM, Sowmya Indrakumar wrote: > 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 > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber -- M.Sc. Andreas Tosstorff Lehrstuhl für Pharmazeutische Technologie und Biopharmazie Department Pharmazie LMU München Butenandtstr. 5-13 ( Haus B) 81377 München Germany Tel.: +49 89 2180 77059 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber

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Received on Mon Mar 27 2017 - 08:30:04 PDT
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