Can you load the mol2 file instead of the pdb file? This seems to work
for me. There may be something wrong with the antechamber step. Can you
post the antechamber command? Have you taken into consideration the
molecules charge?
On 03/28/2017 05:59 PM, Sowmya Indrakumar wrote:
> Hi Andreas,
> PFA the relevant files.
> setup_am1* is the command file to do it for all the protein-ligand complexes. And leap_script1* is the generated file from setup_am1* .
>
> Regards
> Sowmya
>
> ________________________________________
> From: Andreas Tosstorff [andreas.tosstorff.cup.uni-muenchen.de]
> Sent: Tuesday, March 28, 2017 5:45 PM
> To: amber.ambermd.org
> Subject: Re: [AMBER] FEW- issues generating parameter files for MD
>
> Hi Sowmya,
>
>
> could you please share the leap.in file for which you observe the error?
>
>
> On 03/28/2017 05:37 PM, Sowmya Indrakumar wrote:
>> 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
> --
> 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
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Received on Wed Mar 29 2017 - 01:00:03 PDT
