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? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > > >> > > * For (un)subscribe requests visit > >> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > >> > > send a mail to gmx-users-requ...@gromacs.org. > >> > > > >> > -- > >> > 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 > >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> > send a mail to gmx-users-requ...@gromacs.org. > >> > > >> > >> > >> -- > >> *I** have just cycled* from Land's End to John O'Groats (the > >> whole Britain!) > >> for a charity, would you consider supporting my cause? > >> http://uk.virginmoneygiving.com/AlanSilva > >> -- > >> Alan Wilter SOUSA da SILVA, DSc > >> Senior Bioinformatician, UniProt > >> European Bioinformatics Institute (EMBL-EBI) > >> European Molecular Biology Laboratory > >> Wellcome Trust Genome Campus > >> Hinxton > >> Cambridge CB10 1SD > >> United Kingdom > >> Tel: +44 (0)1223 494588 > >> -- > >> 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 > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > 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 > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- *I** have just cycled* from Land's End to John O'Groats (the whole Britain!) for a charity, would you consider supporting my cause? http://uk.virginmoneygiving.com/AlanSilva -- Alan Wilter SOUSA da SILVA, DSc Senior Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.