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 wafa wrote: > > > 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 | > > > > > > > DEBUG: Python Version 3.4.3 (default, Nov 28 2017, 16:41:13) > > [GCC 4.8.4] > > DEBUG: Max execution time tolerance is 10h > > WARNING: no 'babel' executable, no PDB file as input can be used! > > DEBUG: /home/dr/Downloads/amber18/bin/antechamber -i H16.mol2 -fi mol2 -o > > tmp -fo ac -pf y > > DEBUG: > > Welcome to antechamber 17.3: molecular input file processor. > > > > acdoctor mode is on: check and diagnosis problems in the input file. > > -- Check Format for mol2 File -- > >Status: pass > > -- Check Unusual Elements -- > >Status: pass > > -- Check Open Valences -- > >Status: pass > > -- Check Geometry -- > > for those bonded > > for those not bonded > >Status: pass > > -- Check Weird Bonds -- > > /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error! > > Weird atomic valence (3) for atom (ID: 2, Name: C1). > >Possible open valence. > > ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' > > File "../acpype.py", line 3704, in > > File "../acpype.py", line 3392, in __init__ > > File "../acpype.py", line 910, in setResNameCheckCoords > > Total time of execution: less than a second > > > > Looking forward for your suggestions > > Regards > > > > On Thu, Nov 1, 2018 at 10:05 PM Alan wrote: > > > > > 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 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 | > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Thu, 1 Nov 2018 at 19:46, neelam wafa > > > wrote: > > > > > > > > > > > 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: /Users/alan/Programmes/amber16/bin/*antechamber* -i > > H16.mol2 > > > > -fi > > > > > > > mol2 -o tmp -fo ac -pf y > > > > > > > DEBUG: > > > > > > > Warning: the assigned bond types may be wrong, please : > > > > > > > (1) double check the structure (the connectivity) and/or > > > > > > > (2) adjust atom valence penalty parameters in APS.DAT, and/or > > > > > > > (3) increase PSCUTOFF in define.h and recompile bondtype.c > > > > > > > Be cautious, use a large value of PSCUTOFF (>100) will > > > > > significantly > > > > > > > increase the computation time > > > > > > > > > > > > > > > > > > > > > On Thu, 1 Nov 2018 at 08:53, 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 > > > > > > > > File "../acpype.py", line 3392, in __init__ > > > > > > > > File "../acpype.py", line 910, in
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 > 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 | > > > DEBUG: Python Version 3.4.3 (default, Nov 28 2017, 16:41:13) > [GCC 4.8.4] > DEBUG: Max execution time tolerance is 10h > WARNING: no 'babel' executable, no PDB file as input can be used! > DEBUG: /home/dr/Downloads/amber18/bin/antechamber -i H16.mol2 -fi mol2 -o > tmp -fo ac -pf y > DEBUG: > Welcome to antechamber 17.3: molecular input file processor. > > acdoctor mode is on: check and diagnosis problems in the input file. > -- Check Format for mol2 File -- >Status: pass > -- Check Unusual Elements -- >Status: pass > -- Check Open Valences -- >Status: pass > -- Check Geometry -- > for those bonded > for those not bonded >Status: pass > -- Check Weird Bonds -- > /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error! > Weird atomic valence (3) for atom (ID: 2, Name: C1). >Possible open valence. > ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' > File "../acpype.py", line 3704, in > File "../acpype.py", line 3392, in __init__ > File "../acpype.py", line 910, in setResNameCheckCoords > Total time of execution: less than a second > > Looking forward for your suggestions > Regards > > On Thu, Nov 1, 2018 at 10:05 PM Alan wrote: > > > 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 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 | > > > > > > > > > > > > > > > > > > > > > > > > > > On Thu, 1 Nov 2018 at 19:46, neelam wafa > > wrote: > > > > > > > > > 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: /Users/alan/Programmes/amber16/bin/*antechamber* -i > H16.mol2 > > > -fi > > > > > > mol2 -o tmp -fo ac -pf y > > > > > > DEBUG: > > > > > > Warning: the assigned bond types may be wrong, please : > > > > > > (1) double check the structure (the connectivity) and/or > > > > > > (2) adjust atom valence penalty parameters in APS.DAT, and/or > > > > > > (3) increase PSCUTOFF in define.h and recompile bondtype.c > > > > > > Be cautious, use a large value of PSCUTOFF (>100) will > > > > significantly > > > > > > increase the computation time > > > > > > > > > > > > > > > > > > On Thu, 1 Nov 2018 at 08:53, neelam wafa > > > > 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 > > > > > > > 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 > > > > > > >
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 FAILED: [Errno 2] No such file or directory: 'tmp' Total time of execution: less than a second Regards On Fri, Nov 2, 2018 at 7:02 PM neelam wafa wrote: > 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 | > > > DEBUG: Python Version 3.4.3 (default, Nov 28 2017, 16:41:13) > [GCC 4.8.4] > DEBUG: Max execution time tolerance is 10h > WARNING: no 'babel' executable, no PDB file as input can be used! > DEBUG: /home/dr/Downloads/amber18/bin/antechamber -i H16.mol2 -fi mol2 -o > tmp -fo ac -pf y > DEBUG: > Welcome to antechamber 17.3: molecular input file processor. > > acdoctor mode is on: check and diagnosis problems in the input file. > -- Check Format for mol2 File -- >Status: pass > -- Check Unusual Elements -- >Status: pass > -- Check Open Valences -- >Status: pass > -- Check Geometry -- > for those bonded > for those not bonded >Status: pass > -- Check Weird Bonds -- > /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error! > Weird atomic valence (3) for atom (ID: 2, Name: C1). >Possible open valence. > ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' > File "../acpype.py", line 3704, in > File "../acpype.py", line 3392, in __init__ > File "../acpype.py", line 910, in setResNameCheckCoords > Total time of execution: less than a second > > Looking forward for your suggestions > Regards > > On Thu, Nov 1, 2018 at 10:05 PM Alan wrote: > >> 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 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 | >> > > >> > > >> > >> >> > > >> > > >> > > On Thu, 1 Nov 2018 at 19:46, neelam wafa >> wrote: >> > > >> > > > 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: /Users/alan/Programmes/amber16/bin/*antechamber* -i >> H16.mol2 >> > -fi >> > > > > mol2 -o tmp -fo ac -pf y >> > > > > DEBUG: >> > > > > Warning: the assigned bond types may be wrong, please : >> > > > > (1) double check the structure (the connectivity) and/or >> > > > > (2) adjust atom valence penalty parameters in APS.DAT, and/or >> > > > > (3) increase PSCUTOFF in define.h and recompile bondtype.c >> > > > > Be cautious, use a large value of PSCUTOFF (>100) will >> > > significantly >> > > > > increase the computation time >> > > > > >> > > > > >> > > > > On Thu, 1 Nov 2018 at 08:53, neelam wafa >> > > 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 >> > > > > > 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 >>
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 | DEBUG: Python Version 3.4.3 (default, Nov 28 2017, 16:41:13) [GCC 4.8.4] DEBUG: Max execution time tolerance is 10h WARNING: no 'babel' executable, no PDB file as input can be used! DEBUG: /home/dr/Downloads/amber18/bin/antechamber -i H16.mol2 -fi mol2 -o tmp -fo ac -pf y DEBUG: Welcome to antechamber 17.3: molecular input file processor. acdoctor mode is on: check and diagnosis problems in the input file. -- Check Format for mol2 File -- Status: pass -- Check Unusual Elements -- Status: pass -- Check Open Valences -- Status: pass -- Check Geometry -- for those bonded for those not bonded Status: pass -- Check Weird Bonds -- /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error! Weird atomic valence (3) for atom (ID: 2, Name: C1). Possible open valence. ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' File "../acpype.py", line 3704, in File "../acpype.py", line 3392, in __init__ File "../acpype.py", line 910, in setResNameCheckCoords Total time of execution: less than a second Looking forward for your suggestions Regards On Thu, Nov 1, 2018 at 10:05 PM Alan wrote: > 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 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 | > > > > > > > > > > > > > > > > > > On Thu, 1 Nov 2018 at 19:46, neelam wafa > wrote: > > > > > > > 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: /Users/alan/Programmes/amber16/bin/*antechamber* -i H16.mol2 > > -fi > > > > > mol2 -o tmp -fo ac -pf y > > > > > DEBUG: > > > > > Warning: the assigned bond types may be wrong, please : > > > > > (1) double check the structure (the connectivity) and/or > > > > > (2) adjust atom valence penalty parameters in APS.DAT, and/or > > > > > (3) increase PSCUTOFF in define.h and recompile bondtype.c > > > > > Be cautious, use a large value of PSCUTOFF (>100) will > > > significantly > > > > > increase the computation time > > > > > > > > > > > > > > > On Thu, 1 Nov 2018 at 08:53, neelam wafa > > > 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 > > > > > > 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. > > > > > > > > > > > > > > > > > > > > > -- > > > > > *I** have just cycled* from Land's End to John O'Groats (the > > > > > whole Britain!) > > > > > for a charity, would you
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 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 | > > > > > > > > > > > On Thu, 1 Nov 2018 at 19:46, neelam wafa wrote: > > > > > 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: /Users/alan/Programmes/amber16/bin/*antechamber* -i H16.mol2 > -fi > > > > mol2 -o tmp -fo ac -pf y > > > > DEBUG: > > > > Warning: the assigned bond types may be wrong, please : > > > > (1) double check the structure (the connectivity) and/or > > > > (2) adjust atom valence penalty parameters in APS.DAT, and/or > > > > (3) increase PSCUTOFF in define.h and recompile bondtype.c > > > > Be cautious, use a large value of PSCUTOFF (>100) will > > significantly > > > > increase the computation time > > > > > > > > > > > > On Thu, 1 Nov 2018 at 08:53, neelam wafa > > 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 > > > > > 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. > > > > > > > > > > > > > > > > > -- > > > > *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
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? > > > > | ACPYPE: AnteChamber PYthon Parser interfacE v. 2018-09-20T16:44:17UTC (c) > 2018 AWSdS | > > > > > On Thu, 1 Nov 2018 at 19:46, neelam wafa wrote: > > > 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: /Users/alan/Programmes/amber16/bin/*antechamber* -i H16.mol2 -fi > > > mol2 -o tmp -fo ac -pf y > > > DEBUG: > > > Warning: the assigned bond types may be wrong, please : > > > (1) double check the structure (the connectivity) and/or > > > (2) adjust atom valence penalty parameters in APS.DAT, and/or > > > (3) increase PSCUTOFF in define.h and recompile bondtype.c > > > Be cautious, use a large value of PSCUTOFF (>100) will > significantly > > > increase the computation time > > > > > > > > > On Thu, 1 Nov 2018 at 08:53, neelam wafa > 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 > > > > 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. > > > > > > > > > > > > > -- > > > *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
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 | On Thu, 1 Nov 2018 at 19:46, neelam wafa wrote: > 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: /Users/alan/Programmes/amber16/bin/*antechamber* -i H16.mol2 -fi > > mol2 -o tmp -fo ac -pf y > > DEBUG: > > Warning: the assigned bond types may be wrong, please : > > (1) double check the structure (the connectivity) and/or > > (2) adjust atom valence penalty parameters in APS.DAT, and/or > > (3) increase PSCUTOFF in define.h and recompile bondtype.c > > Be cautious, use a large value of PSCUTOFF (>100) will significantly > > increase the computation time > > > > > > On Thu, 1 Nov 2018 at 08:53, neelam wafa 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 > > > 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. > > > > > > > > > -- > > *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.
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: /Users/alan/Programmes/amber16/bin/*antechamber* -i H16.mol2 -fi > mol2 -o tmp -fo ac -pf y > DEBUG: > Warning: the assigned bond types may be wrong, please : > (1) double check the structure (the connectivity) and/or > (2) adjust atom valence penalty parameters in APS.DAT, and/or > (3) increase PSCUTOFF in define.h and recompile bondtype.c > Be cautious, use a large value of PSCUTOFF (>100) will significantly > increase the computation time > > > On Thu, 1 Nov 2018 at 08:53, neelam wafa 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 > > 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. > > > > > -- > *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.
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 assigned bond types may be wrong, please : (1) double check the structure (the connectivity) and/or (2) adjust atom valence penalty parameters in APS.DAT, and/or (3) increase PSCUTOFF in define.h and recompile bondtype.c Be cautious, use a large value of PSCUTOFF (>100) will significantly increase the computation time On Thu, 1 Nov 2018 at 08:53, neelam wafa 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 > 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. > -- *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.
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 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 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 > > 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.
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, at 09:52, neelam wafa 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 > 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.
