Hi Andreas,
The leap file I sent is for generating the *lib file for the ligand. That worked fine for me as well.
The PDB you mentioned about is mentioned while creating the parameter file for the protein-ligand complex. The leap.* for that is a different one. I get the error during this step.
Regards
Sowmya
________________________________________
From: Andreas Tosstorff [andreas.tosstorff.cup.uni-muenchen.de]
Sent: Tuesday, March 28, 2017 4:24 PM
To: AMBER Mailing List
Subject: Re: [AMBER] FEW- issues generating parameter files for MD
Hi Sowmya,
I cannot reproduce your error. The only thing I changed were the
filepaths in your tleap.in file and it works fine. The error log you
send states that you are loading a pdb file, however in the tleap.in
file you send you are loading a mol2 file. Could this be the problem?
Best,
Andy
On 03/28/2017 11:26 AM, Sowmya Indrakumar wrote:
> Hi Andreas,
> PFA the files you asked for.
> Thanks
> Regards
> Sowmya
> ________________________________________
> From: Andreas Tosstorff [andreas.tosstorff.cup.uni-muenchen.de]
> Sent: Monday, March 27, 2017 5:28 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] FEW- issues generating parameter files for MD
>
> 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
>>>
>>>
>>> _______________________________________________
>>> 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
>>
>>
>> _______________________________________________
>> 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
>
>
> _______________________________________________
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 28 2017 - 09:00:02 PDT
