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
>
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Received on Sun Dec 16 2018 - 17:00:03 PST
