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 - 06:30:03 PST
