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
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Received on Tue Mar 28 2017 - 09:00:04 PDT
