Hi Seke,
I'd try adding a '2' tp 'parmchk' in whatever script is running, and if
it seems to work watch for other problems in case usage or assumptions
have changed. I'm not familiar with the code myself, but you may find
useful discussion in the archives.
Bill
On 12/16/18 4:31 PM, Seketoulie Keretsu wrote:
> Dear Bill,
>
> Thank you for the response. I have executed the environment setup
> script (sanders, tleap etc can be called from console). I noticed in
> the error report that "parmchk" has failed. Interestingly, in
> Amber2018 (i.e $AMBERHOME/bin) the "parmchk2" is available not
> "parmchk". Hence if acpype is looking for parmchk, this could be a
> problem. I could be very wrong. Kindly advise.
>
> The error report is shown below:
> ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> /bin/sh: -c: line 0: syntax error near unexpected token `('
> /bin/sh: -c: line 0: `which: no parmchk in
> (/home/main/Downloads/amber18/bin:/home/main/Downloads/amber18/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/usr/local/gromacs/bin:/home/main/.local/bin:/home/main/bin:/usr/local/gromacs/bin)
> -i Ligand_bcc_gaff.mol2 -f mol2 -o Ligand_AC.frcmod'
> ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> ERROR: Parmchk failed
> ERROR: Tleap failed
> ==> ... trying Sleap
> ==> Executing Sleap...
> ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> Thank you. Seke
>
> On Sun, Dec 16, 2018 at 11:10 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
>> Did you run the environment setup script? amber.sh for bash I think.
>>
>> Bill
>>
>> <div>-------- Original message --------</div><div>From: Seketoulie Keretsu <sekekeretsu.gmail.com> </div><div>Date:12/16/2018 5:58 AM (GMT-08:00) </div><div>To: amber.ambermd.org </div><div>Subject: [AMBER] Acpype related problem : topology for GROMACS </div><div>
>> </div>Dear Expert,
>>
>> I came this problem while trying to generate ligand topology for use Gromacs.
>> I have gromacs 2018 and also amber installed in my system (CentOS7).
>>
>> I installed acpype by extracting the .tar file and "python setup.py install".
>>
>> I am following the tutorial give in this link:
>> https://code.google.com/archive/p/acpype/wikis/TutorialAcpype4Gromacs.wiki
>>
>> The error report is shown below.
>>
>> [main.localhost try1]$ acpype -i Ligand.pdb
>> ============================================================================
>> | ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2018 AWSdS |
>> ============================================================================
>> ==> ... charge set to 0
>> ==> ... converting pdb input file to mol2 input file
>> ==> * Babel OK *
>> ==> Executing Antechamber...
>> ==> * Antechamber OK *
>> ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> /bin/sh: -c: line 0: syntax error near unexpected token `('
>> /bin/sh: -c: line 0: `which: no parmchk in
>> (/home/main/Downloads/amber18/bin:/home/main/Downloads/amber18/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/usr/local/gromacs/bin:/home/main/.local/bin:/home/main/bin:/usr/local/gromacs/bin)
>> -i Ligand_bcc_gaff.mol2 -f mol2 -o Ligand_AC.frcmod'
>> ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> ERROR: Parmchk failed
>> ERROR: Tleap failed
>> ==> ... trying Sleap
>> ==> Executing Sleap...
>> ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>
>> ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> /bin/sh: -c: line 0: syntax error near unexpected token `('
>> /bin/sh: -c: line 0: `which: no sleap in
>> (/home/main/Downloads/amber18/bin:/home/main/Downloads/amber18/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/usr/local/gromacs/bin:/home/main/.local/bin:/home/main/bin:/usr/local/gromacs/bin)
>> -f sleap.in'
>>
>> ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> ERROR: Sleap failed
>> ==> Removing temporary files...
>> ACPYPE FAILED: [Errno 2] No such file or directory: 'Ligand_AC.prmtop'
>> Total time of execution: 12m 43s
>>
>> What could be the problem here and how do i rectify this ??
>>
>> Thank you.
>>
>> Sincerely, Seke
>>
>> _______________________________________________
>> 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
> _______________________________________________
> 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 Sun Dec 16 2018 - 19:00:03 PST
