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.