Do you have the charges set inside your mol2 file?
Which acpype version are you using? Be sure to be using the latest, which
you can get by:
git clone https://github.com/alanwilter/acpype.git
If still having problems, please run:
acpype -di ligand.mol2 -c user # -d is for debug mode
and send
Ok thanks.
On Sat, 3 Nov 2018, 1:46 pm Alan Ok, I'm still using Amber16, yours is 2018. I believe that they made FATAL
> error now the warning we used to have with 2016 version.
>
> There's nothing I can do. Please, seek Amber mailing list help.
>
> Alan
>
> On Fri, 2 Nov 2018 at 19:03, neelam
Ok, I'm still using Amber16, yours is 2018. I believe that they made FATAL
error now the warning we used to have with 2016 version.
There's nothing I can do. Please, seek Amber mailing list help.
Alan
On Fri, 2 Nov 2018 at 19:03, neelam wafa wrote:
> Hi!
> This is the command I use
>
If I don't use -d then this is the result:
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2018-09-20T16:44:17UTC (c)
2018 AWSdS |
WARNING: no 'babel' executable, no PDB file as input can be used!
ACPYPE
Hi!
This is the command I use
dr@dr-HP-1000-Notebook-PC:~/Downloads/acpype/test$ ../acpype.py -di
H16.mol2 -c gas
and the output is:
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2018-09-20T16:44:17UTC (c)
2018 AWSdS |
Please, post here the command you're using (add -d anyway for debug) and
show the whole output.
Thanks,
Alan
On Thu, 1 Nov 2018 at 20:04, neelam wafa wrote:
> Yes it the same one. And the tests are running okay. Problem is with my
> files.
>
> On Fri, 2 Nov 2018, 12:56 am Alan
> > Indeed, it
Yes it the same one. And the tests are running okay. Problem is with my
files.
On Fri, 2 Nov 2018, 12:56 am Alan Indeed, it worked, though the warning is important. Are you using the
> latest ACPYPE?
>
>
>
>
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 |
Means this file worked well on your system?
On Fri, 2 Nov 2018, 12:38 am Alan 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:
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
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.
On Thu, 1 Nov 2018, 4:46 pm Ali Khodayari Have you tried to source amber
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.
> On 1 Nov 2018,
I have by defalt python 2.7.6
and python 3.4.3
Regards
On Tue, 30 Oct 2018, 1:11 am Alan, wrote:
> Are you running python3?
>
> what
>
> python -V
>
> or
>
> python3 -V
>
> outputs?
>
> Alan
>
> On Mon, 29 Oct 2018 at 13:25, neelam wafa wrote:
>
> > Hi
> > Thanks for your help. I have
Are you running python3?
what
python -V
or
python3 -V
outputs?
Alan
On Mon, 29 Oct 2018 at 13:25, neelam wafa wrote:
> Hi
> Thanks for your help. I have resolved that problem but got another one .
> when I run the command
>
> ../acpype.py -i FFF.pdb
>
> I get this error.
> File
Hi
Thanks for your help. I have resolved that problem but got another one .
when I run the command
../acpype.py -i FFF.pdb
I get this error.
File "../acpype.py", line 561
def __init__(self) -> None:
^
SyntaxError: invalid syntax
can you please help me out of the
Hi Farial,
Are you online now?
Bhupendra
On Mon, Oct 29, 2018 at 12:10 PM Farial Tavakoli
wrote:
> Dear Bhupendra
>
> Thanks for your reply
>
> I am in /Downloads/acpype-master/acpype/scripts path and type only acpype
> -h or acpype.py -h , but face with this error:
> acpype: command not
Check your python3, what's the command line for your python3?
The shebang line (first line) in acpype.py is:
#!/usr/bin/env python3
you need python3 to run acpype. If your default python is already python3,
then change line to
#!/usr/bin/env python
python -V
tells which python version you
Hi, Alan
I have installed amber tools 18 for antechamber and acpype with
git clone https://github.com/alanwilter/acpype.git
then installed it with
ln -s $PWD/acpype.py /usr/local/bin/acpype
I didn't install open babel because my input files are in mol2 format.
when i reun the command acpype
We are working on it now. I can't tell you exactly because we need several
tests. It's a complete new version re-written from scratch.
I'm really sorry for the inconvenience but we hope to bring it back in a
month or two.
Alan
On Wed, 24 Oct 2018 at 16:58, neelam wafa wrote:
> Hi alan
>
> Can
Hi alan
Can you please tell how long will it take for the online acpype server to
be available?
Regards
Neelam wafa
On Wed, 24 Oct 2018, 6:23 pm Alan, wrote:
> Indeed, it's mostly Luciano spearheading these new things. Hopefully, we
> will have more things to show eventually.
>
> Alan
>
> On
Indeed, it's mostly Luciano spearheading these new things. Hopefully, we
will have more things to show eventually.
Alan
On Wed, 24 Oct 2018 at 14:14, Bhupendra Dandekar <
bhupendra.dandekar...@gmail.com> wrote:
> I actually got lot of help from Luciano Kagami about installation and usage
> of
I actually got lot of help from Luciano Kagami about installation and usage
of acpype and ligro.
Thanks to both of you.
Bhupendra
On Wed, Oct 24, 2018 at 6:38 PM Bhupendra Dandekar <
bhupendra.dandekar...@gmail.com> wrote:
> Thanks to you also sir.
> Your work is really appreciated and is
Thanks to you also sir.
Your work is really appreciated and is really helpful.
Bhupendra
On Wed, Oct 24, 2018 at 3:59 PM Alan wrote:
> Thanks Bhupendra, indeed we have this option, which is experimental, but
> I'm glad to see some are already using it and it seems to be working.
>
> Alan
>
>
Thanks Bhupendra, indeed we have this option, which is experimental, but
I'm glad to see some are already using it and it seems to be working.
Alan
On Wed, 24 Oct 2018 at 11:20, Bhupendra Dandekar <
bhupendra.dandekar...@gmail.com> wrote:
> Dear Farial,
>
> Use this command to install acpype
Dear Farial,
Use this command to install acpype and antechamber using conda:
conda install -c acpype -c openbabel -c ambermd
and then you can check and call acpype, antechamber like this from your
terminal:
acpype -h
antechamber -h
then you can generate ligand topology using this command:
Latest acpype is here: https://github.com/alanwilter/acpype
Mind that it's *only* Python 3 compatible now.
Run something like this, at first, to be sure:
_full_to_your_python3 _full_path_to_acpype -d -i ...
You need Antechamber (from Amber) if you want to generate topologies.
Only if
Hi
Cool, is there any article or citation for GAFF2?
Best wishes
Anders
On Tue, Jan 17, 2017 at 7:44 PM, Alan wrote:
> Now one can do:
>
> acpype -a gaff2 -i ...
>
> See 'acpype -h' for more details:
>
> -a ATOM_TYPE, --atom_type=ATOM_TYPE
>
On 2/29/16 4:51 AM, Abid Channa wrote:
Dear Gromacs users,
I am going to run complex simulation. I have prepared ligand topology through acpype ,
from where I have taken two files .gro and .itp file. I have used Gromos ff for my
simulation . I got atom type error while running this command
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