Re: [gmx-users] acpype error

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

[gmx-users] acpype error

I installed acpype to generate the necessary files of  ligand.if I use this command: "Acpype -i ligand.mol2 -c user" I will get following message:"ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp'" Please guide meThanks a lot -- Gromacs Users mailing list * Please search the

Re: [gmx-users] ACPYPE not working.

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

Re: [gmx-users] ACPYPE not working.

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 >

Re: [gmx-users] ACPYPE not working.

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

Re: [gmx-users] ACPYPE not working.

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 |

Re: [gmx-users] ACPYPE not working.

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

Re: [gmx-users] ACPYPE not working.

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? > > > >

Re: [gmx-users] ACPYPE not working.

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 |

Re: [gmx-users] ACPYPE not working.

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:

Re: [gmx-users] ACPYPE not working.

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

Re: [gmx-users] ACPYPE not working.

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

Re: [gmx-users] ACPYPE not working.

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,

[gmx-users] ACPYPE not working.

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

[gmx-users] acpype is not working

Dear all I am trying to convert .oFF and .FRCMOD format files to the format that is compatible with GMX format, so I installed anaconda to use conda install -c acpype -c openbabel -c ambermd command because I did not install amber and openbabel programs. then issued this command: conda install -c

[gmx-users] Acpype and antechamber

Hi Bhupendra Thank you for your reply You asked me yesterday “Are you on line now? “ and I replied “ yes I am on line “ Anyway, I issued this command : " conda install -c acpype -c openbabel -c antechambermd python=3.7 and the system replied : "Solving environment: done # All requested packages

[gmx-users] Acpype failed Errno2

Hi I am using acpype . I have amber tools 18. I get an error. When I run my ligand file for topology i got ACPYPE failed: Errno 2 no such file or directory: 'temp'. Any suggestion for the problem . Thanks in advance. Regards Show quoted text -- Gromacs Users mailing list * Please search the

Re: [gmx-users] acpype

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

Re: [gmx-users] acpype

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

Re: [gmx-users] acpype

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

Re: [gmx-users] acpype and conda

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

[gmx-users] acpype and conda

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 found I can run acpype only when type python command before it. In addition, I installed

Re: [gmx-users] acpype

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

Re: [gmx-users] acpype

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

Re: [gmx-users] 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

Re: [gmx-users] acpype

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

[gmx-users] acpype

Dear Justin I installed acpype on the ubuntu but didnt install Antechamber and openbable . Now I am trying to convert the AMBER parameters format (obtained from  http://sites.pharmacy.manchester.ac.uk/bryce/amber  ) to the one that gromacs is compatible with in the .rtp files. I pasted acpype.py

Re: [gmx-users] acpype

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

Re: [gmx-users] acpype

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

Re: [gmx-users] acpype

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 > >

Re: [gmx-users] acpype

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

Re: [gmx-users] 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:

Re: [gmx-users] acpype

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

[gmx-users] acpype

Dear GMX useres I am trying to convert .OFF and .FRCMOD files obtained from AMBER parameter database (Bryce Group: Computational Biophysics and Drug Design - University of Manchester) to the format that GROMACS is compatible with in .rtp

[gmx-users] acpype

Dear GMX useres I am trying to convert .OFF and .FRCMOD files obtained from AMBER parameter database (Bryce Group: Computational Biophysics and Drug Design - University of Manchester) to the format that GROMACS is compatible with in .rtp files. so referred to GROMACS tutorial protein-ligand

Re: [gmx-users] ACPYPE now works with GAFF2

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 >

[gmx-users] ACPYPE now works with GAFF2

Now one can do: acpype -a gaff2 -i ... See 'acpype -h' for more details: -a ATOM_TYPE, --atom_type=ATOM_TYPE atom type, can be gaff, gaff2, amber (AMBER14SB) or amber2 (AMBER14SB + GAFF2), default is gaff Thanks for using ACPYPE, Alan --

Re: [gmx-users] Acpype topolgy error

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

[gmx-users] Acpype topolgy error

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  " gmx grompp -f em.mdp -c solv.gro -p

[gmx-users] acpype problem

Hi; I want to convert amber topology and coordinate files into gromacs topology and coordinate file with the acpype command ( acpype -p FFF_AC.prmtop -x FFF_AC.inpcrd ), but when I type it, I get this error: acpype: command not found I've done the procedure mentioned in the website: