Please also share the .lib file
On 03/27/2017 05:18 PM, Sowmya Indrakumar wrote:
> 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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>> 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
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> 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
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Received on Mon Mar 27 2017 - 08:30:05 PDT
