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