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 <ali.khoday...@student.kuleuven.be wrote: > 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, at 09:52, neelam wafa <neelam.w...@gmail.com> wrote: > > > > 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 > > /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error! > > Weird atomic valence (2) for atom (ID: 1, Name: C). > > Possible open valence. > > ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' > > File "../acpype.py", line 3704, in <module> > > File "../acpype.py", line 3392, in __init__ > > File "../acpype.py", line 910, in setResNameCheckCoords > > Total time of execution: less than a second > > Please any way to get out of this problem? Looking forward for your > > cooperation > > Regards > > -- > > 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. -- 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.