subject:"Re\: \[gmx\-users\] acpype"

Re: [gmx-users] acpype error

2019-07-10 Thread Alan

Do you have the charges set inside your mol2 file?

Which acpype version are you using? Be sure to be using the latest, which
you can get by:

git clone https://github.com/alanwilter/acpype.git

If still having problems, please run:

acpype -di ligand.mol2 -c user # -d is for debug mode

and send it to me, with your input file if you don't mind.

Thanks for using ACPYPE.

Best regards

Alan

On Wed, 10 Jul 2019 at 07:57, Mahboobeh Eslami 
wrote:

> I installed acpype to generate the necessary files of  ligand.if I use
> this command:
> "Acpype -i ligand.mol2 -c user"
>
> I will get following message:"ACPYPE FAILED: [Errno 2] No such file or
> directory: 'tmp'"
> Please guide meThanks a lot
>
>
>
> --
> 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
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
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-- 
Wanna help a great cause? Please:
*https://www.raymondnicolettrust.com/events/2019/11/1/pbp2019
*
And many thanks!

Alan ‍♂‍♂
-- 
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Re: [gmx-users] ACPYPE not working.

2018-11-03 Thread neelam wafa

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.

2018-11-03 Thread 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 
> > > > 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.

2018-11-02 Thread neelam wafa

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.

2018-11-02 Thread neelam wafa

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.

2018-11-01 Thread Alan

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.

2018-11-01 Thread neelam wafa

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.

2018-11-01 Thread 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

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] ACPYPE not working.

2018-11-01 Thread neelam wafa

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!

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] ACPYPE not working.

2018-11-01 Thread 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

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] ACPYPE not working.

2018-11-01 Thread neelam wafa

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
>
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Re: [gmx-users] ACPYPE not working.

2018-11-01 Thread 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.
-- 
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* Please search the archive at 
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* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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Re: [gmx-users] acpype

2018-10-30 Thread neelam wafa

I have by defalt python 2.7.6

and python 3.4.3

Regards

On Tue, 30 Oct 2018, 1:11 am Alan,  wrote:

> Are you running python3?
>
> what
>
> python -V
>
> or
>
> python3 -V
>
> outputs?
>
> Alan
>
> On Mon, 29 Oct 2018 at 13:25, neelam wafa  wrote:
>
> > 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  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 
> 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  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 
> > > 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,  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  >
> > > > 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,

Re: [gmx-users] acpype

2018-10-29 Thread Alan

Are you running python3?

what

python -V

or

python3 -V

outputs?

Alan

On Mon, 29 Oct 2018 at 13:25, neelam wafa  wrote:

> 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  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  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  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 
> > 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,  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 
> > > 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
> > > > > -
> > > > > > > >>

Re: [gmx-users] acpype

2018-10-29 Thread neelam wafa

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  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  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  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 
> 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,  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 
> > 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)
> > > > > > >> > >  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
> > > >

Re: [gmx-users] acpype and conda

2018-10-29 Thread Bhupendra Dandekar

Hi Farial,
Are you online now?

Bhupendra

On Mon, Oct 29, 2018 at 12:10 PM Farial Tavakoli 
wrote:

>  Dear Bhupendra
>
> Thanks for your reply
>
> I am in /Downloads/acpype-master/acpype/scripts path and type only acpype
> -h or acpype.py -h , but face with this error:
> acpype: command not found
> I can run acpype only when type python command before it.
> In addition, I installed Anaconda2-5.3.0-Linux-x86_64.sh on "/home/vaio"
> yesterday and issued the "conda install -c acpype -c openbabel -c ambermd"
> command
> but faced with this error:
>  CondaValueError: too few arguments, must supply command line package specs
>  or --file
>  python version = python 2.7.15
> Would you please help me ? I dont know how I should deal with these
> problems.
>
> Thanks in advance
> 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
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
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Re: [gmx-users] acpype

2018-10-25 Thread Alan

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  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  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  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,  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 
> 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)
> > > > > >> > >  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

Re: [gmx-users] acpype

2018-10-25 Thread neelam wafa

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  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  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,  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  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)
> > > > >> > >  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
>

Re: [gmx-users] acpype

2018-10-24 Thread Alan

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  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,  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  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)
> > > >> > >  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

Re: [gmx-users] acpype

2018-10-24 Thread neelam wafa

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,  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  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)
> > >> > >  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
> > >>

Re: [gmx-users] acpype

2018-10-24 Thread Alan

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  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)
> >> > >  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

Re: [gmx-users] acpype

2018-10-24 Thread Bhupendra Dandekar

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  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)
>> > >  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.
>
>
-- 
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* 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

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Re: [gmx-users] acpype

2018-10-24 Thread Bhupendra Dandekar

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  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)
> > >  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.
-- 
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* 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
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] acpype

2018-10-24 Thread Alan

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  >
> 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)
> >  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.

Re: [gmx-users] acpype

2018-10-24 Thread Bhupendra Dandekar

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 
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)
>  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.
>
-- 
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* 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
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] acpype

2018-10-24 Thread Alan

Latest acpype is here: https://github.com/alanwilter/acpype

Mind that it's *only* Python 3 compatible now.

Run something like this, at first, to be sure:

_full_to_your_python3 _full_path_to_acpype -d -i ...

You need Antechamber (from Amber) if you want to generate topologies.

Only if converting from Amber to GMX that you do not need Antechamber (but
if you play with AMBER format, you certainly have AmberTools installed,
right?)

I hope it helps,

Alan

On Wed, 24 Oct 2018 at 09:31, Farial Tavakoli 
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)
>  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*
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> Gromacs Users mailing list
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-- 
*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
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Re: [gmx-users] ACPYPE now works with GAFF2

2017-01-17 Thread Anders Støttrup Larsen

Hi


Cool, is there any article or citation for GAFF2?

Best wishes


Anders

On Tue, Jan 17, 2017 at 7:44 PM, Alan  wrote:

> Now one can do:
>
> acpype -a gaff2 -i ...
>
> See 'acpype -h' for more details:
>
>   -a ATOM_TYPE, --atom_type=ATOM_TYPE
> atom type, can be gaff, gaff2, amber (AMBER14SB) or
> amber2 (AMBER14SB + GAFF2), default is gaff
>
> Thanks for using ACPYPE,
>
> Alan
>
> --
> 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
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Re: [gmx-users] Acpype topolgy error

2016-02-29 Thread Justin Lemkul




On 2/29/16 4:51 AM, Abid Channa wrote:

Dear Gromacs users,
I am going to run complex simulation. I have prepared ligand topology through acpype , 
from where I have taken two files .gro and .itp file. I have used Gromos ff for my 
simulation . I got atom type error while running this command  " gmx grompp -f 
em.mdp -c solv.gro -p topol.top -o ions.tpr". My acpype taken .itp file is like [ 
atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot   
bond_type
  1   ca 1   THAC11-0.119000 12.01000 ; qtot -0.119
  2   ca 1   THAC22-0.173300 12.01000 ; qtot -0.292
  3   ca 1   THAC33 0.430600 12.01000 ; qtot 0.138
  4   ca 1   THAC44-0.182300 12.01000 ; qtot -0.044
  5   ca 1   THAC55-0.105000 12.01000 ; qtot -0.149It 
gave following error
Fatal error:
Atomtype ca not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Kindly suggest me How can I resolve this problem.



There are probably new [atomtypes] in the topology that you haven't included. 
Atom types are case-sensitive and lowercase types are often used to avoid 
conflicts with the parent force field.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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