[gmx-users] ACPYPE not working.

Discussion:

neelam wafa

2018-11-01 08:52:46 UTC

Hi!
Dear all
I am using acpype to generate topologies of ligand for gromacs md
simmulation. I habe amber tools 18 and downloaded acpype from github. The
test runs go well but when i run my file with ../acpype.py -i UNL.mol2 -c
gas or even
../acpype.py -di UNL.mol2
iI get following error
/home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
Weird atomic valence (2) for atom (ID: 1, Name: C).
Possible open valence.
ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp'
File "../acpype.py", line 3704, in <module>
File "../acpype.py", line 3392, in __init__
File "../acpype.py", line 910, in setResNameCheckCoords
Total time of execution: less than a second
Please any way to get out of this problem? Looking forward for your
cooperation
Regards

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Ali Khodayari

2018-11-01 11:45:38 UTC

Permalink

Have you tried to source amber before commanding acpype for the conversion?
Apparently it’s looking for antechamber but it can’t access it.
When amber is sourced first, you can get a result from commands such as antechamber -h
Try to first source your amber, and then run acpype.

Post by neelam wafa
Hi!
Dear all
I am using acpype to generate topologies of ligand for gromacs md
simmulation. I habe amber tools 18 and downloaded acpype from github. The
test runs go well but when i run my file with ../acpype.py -i UNL.mol2 -c
gas or even
../acpype.py -di UNL.mol2
iI get following error
/home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
Weird atomic valence (2) for atom (ID: 1, Name: C).
Possible open valence.
ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp'
File "../acpype.py", line 3704, in <module>
File "../acpype.py", line 3392, in __init__
File "../acpype.py", line 910, in setResNameCheckCoords
Total time of execution: less than a second
Please any way to get out of this problem? Looking forward for your
cooperation
Regards
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* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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neelam wafa

2018-11-01 12:14:27 UTC

Permalink

Yes i have sourced antechamber and both antechamber -h and acpype -h
command work. When i run command
acpype.py -i ligand.mol2
It says no such file or directory 'temp'
With acpype.py -di ligand.mol2 its gives above error.

Post by Ali Khodayari
Have you tried to source amber before commanding acpype for the conversion?
Apparently it’s looking for antechamber but it can’t access it.
When amber is sourced first, you can get a result from commands such as antechamber -h
Try to first source your amber, and then run acpype.

-c

Post by neelam wafa
gas or even
../acpype.py -di UNL.mol2
iI get following error
/home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
Weird atomic valence (2) for atom (ID: 1, Name: C).
Possible open valence.
ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp'
File "../acpype.py", line 3704, in <module>
File "../acpype.py", line 3392, in __init__
File "../acpype.py", line 910, in setResNameCheckCoords
Total time of execution: less than a second
Please any way to get out of this problem? Looking forward for your
cooperation
Regards
--
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* Please search the archive at

http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

Post by neelam wafa
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Alan

2018-11-01 19:37:40 UTC

Permalink

This kind of problem is due to ANTECHAMBER, not ACPYPE. You may try to get
help at AMBER mailing list.

For an example I was given, running here:
acpype -di H16.mol2 -c gas

DEBUG: /Users/alan/Programmes/amber16/bin/*antechamber* -i H16.mol2 -fi
mol2 -o tmp -fo ac -pf y
DEBUG:
Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase PSCUTOFF in define.h and recompile bondtype.c
Be cautious, use a large value of PSCUTOFF (>100) will significantly
increase the computation time

Post by neelam wafa
Hi!
Dear all
I am using acpype to generate topologies of ligand for gromacs md
simmulation. I habe amber tools 18 and downloaded acpype from github. The
test runs go well but when i run my file with ../acpype.py -i UNL.mol2 -c
gas or even
../acpype.py -di UNL.mol2
iI get following error
/home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
Weird atomic valence (2) for atom (ID: 1, Name: C).
Possible open valence.
ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp'
File "../acpype.py", line 3704, in <module>
File "../acpype.py", line 3392, in __init__
File "../acpype.py", line 910, in setResNameCheckCoords
Total time of execution: less than a second
Please any way to get out of this problem? Looking forward for your
cooperation
Regards
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
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neelam wafa

2018-11-01 19:45:54 UTC

Permalink

Means this file worked well on your system?

Post by Alan
This kind of problem is due to ANTECHAMBER, not ACPYPE. You may try to get
help at AMBER mailing list.
acpype -di H16.mol2 -c gas
DEBUG: /Users/alan/Programmes/amber16/bin/*antechamber* -i H16.mol2 -fi
mol2 -o tmp -fo ac -pf y
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase PSCUTOFF in define.h and recompile bondtype.c
Be cautious, use a large value of PSCUTOFF (>100) will significantly
increase the computation time

-c

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whole Britain!)
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United Kingdom
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Alan

2018-11-01 19:55:28 UTC

Permalink

Indeed, it worked, though the warning is important. Are you using the
latest ACPYPE?

========================================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2018-09-20T16:44:17UTC (c)
2018 AWSdS |
========================================================================================

Post by neelam wafa
Means this file worked well on your system?

Post by Alan
This kind of problem is due to ANTECHAMBER, not ACPYPE. You may try to

get

Post by Alan
help at AMBER mailing list.
acpype -di H16.mol2 -c gas
DEBUG: /Users/alan/Programmes/amber16/bin/*antechamber* -i H16.mol2 -fi
mol2 -o tmp -fo ac -pf y
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase PSCUTOFF in define.h and recompile bondtype.c
Be cautious, use a large value of PSCUTOFF (>100) will significantly
increase the computation time

Post by neelam wafa
Hi!
Dear all
I am using acpype to generate topologies of ligand for gromacs md
simmulation. I habe amber tools 18 and downloaded acpype from github.

The