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 situation? Thanks in advance Regards On Thu, Oct 25, 2018 at 4:02 PM Alan <alanwil...@gmail.com> wrote: > 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 have. > > Thanks, > > Alan > > On Thu, 25 Oct 2018 at 16:44, neelam wafa <neelam.w...@gmail.com> wrote: > > > 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 -h or acpype i ligand.mol2 > > > > it says, acpype command not found. > > > > please help me about how to use acpype to generate ligand topology as > > i have been the online acpype server for the purpose. > > > > thanks in advance. > > > > Regards > > > > > > On Wed, Oct 24, 2018 at 9:29 PM Alan <alanwil...@gmail.com> wrote: > > > > > 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 <neelam.w...@gmail.com> > wrote: > > > > > > > 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, <alanwil...@gmail.com> wrote: > > > > > > > > > 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 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 really helpful. > > > > > > > > > > > > > > > > > > > > > Bhupendra > > > > > > > > > > > > > > On Wed, Oct 24, 2018 at 3:59 PM Alan <alanwil...@gmail.com> > > 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 > > > > > > >> > > > > > > >> On Wed, 24 Oct 2018 at 11:20, Bhupendra Dandekar < > > > > > > >> bhupendra.dandekar...@gmail.com> wrote: > > > > > > >> > > > > > > >> > 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: > > > > > > >> > > > > > > > >> > acpype -i FFF.pdb -b FFF -o gmx > > > > > > >> > > > > > > > >> > Hope this helps. Let me know if you have any questions. > > > > > > >> > > > > > > > >> > Thanks > > > > > > >> > Bhupendra > > > > > > >> > > > > > > > >> > On Wed, Oct 24, 2018 at 2:01 PM Farial Tavakoli < > > > > > > >> faryal.tavak...@gmail.com > > > > > > >> > > > > > > > > >> > wrote: > > > > > > >> > > > > > > > >> > > 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) > > > > > > >> > > <http://sites.pharmacy.manchester.ac.uk/bryce/amber> to > the > > > > > format > > > > > > >> that > > > > > > >> > > GROMACS is compatible with in .rtp files*. so referred to > > > > GROMACS > > > > > > >> > tutorial > > > > > > >> > > protein-ligand complex and downloaded acpype. installed it > > > using > > > > > its > > > > > > >> > > readme.txt file but whenever i typed ../acpype.py -i > > > FFF.pdb > > > > > At > > > > > > >> > folder > > > > > > >> > > *acpype/test* (/Downloads/acpype-master/acpype) or > > > > > > >> > > (/Downloads/acpype-master/acpype/test) faced to this > error:* > > > > > > >> > > > > > > > > >> > > > > > > > > >> > > *bash: ../acpype.py: No such file or directory* > > > > > > >> > > > > > > > > >> > > *while when I typed whereis acpype in terminal , the > > operating > > > > > > system > > > > > > >> > says > > > > > > >> > > :* > > > > > > >> > > > > > > > > >> > > > > > > > > >> > > *acpype: /usr/local/bin/acpype* > > > > > > >> > > * it means there is the executable file of acpype . so how > > > come > > > > I > > > > > > type > > > > > > >> > > ../acpype.py -h or ../acpype -i FFF.pdb , the system says > NO > > > > such > > > > > > >> file or > > > > > > >> > > directory?* > > > > > > >> > > *Is there anyone who ca help me?* > > > > > > >> > > *I really would be appreciated it if one help me to solve > > this > > > > and > > > > > > can > > > > > > >> > > convert the AMBER format files to GRMACS format files.* > > > > > > >> > > > > > > > > >> > > *best regards* > > > > > > >> > > *Farial* > > > > > > >> > > -- > > > > > > >> > > Gromacs Users mailing list > > > > > > >> > > > > > > > > >> > > * Please search the archive at > > > > > > >> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > > > > > before > > > > > > >> > > posting! > > > > > > >> > > > > > > > > >> > > * Can't post? 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