Re: [gmx-users] Multi-GPU optimization, "DD without halo exchange is not supported"

[Alan Gray]

Hi Leandro,

I see from your command line that you are using an external MPI library and 
running gmx_mpi via mpirun. The new GPU communication features are currently 
only supported with use of thread MPI (see 
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multithreading_with_thread-MPI),
 and this therefore means only within a single compute node. (It looks like we 
need better reporting on this.) We have removed this limitation in a branch of 
the development repository at 
https://gitlab.com/gromacs/gromacs/-/merge_requests/37, but this still needs 
some more work before it is merged into the master branch.

I also see that you are using 16 MPI tasks - I suspect that (regardless of the 
new GPU features) your case might not scale this high since it will be limited 
by the single PME MPI task, but it is best to experiment and tune these options 
(similarly for -nstlist and -ntomp, as Szilard already mentioned).

Best regards,

Alan

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Re: [gmx-users] question on dihedrals propers func 3 and impropers func 1

[Alan]

Which version of ACPYPE are you using? Please, get the latest here:
https://github.com/alanwilter/acpype

Check also about option:

-z, --gmx4write RB dihedrals old GMX 4.0

Thanks for using ACPYPE!

Alan

On Sat, 1 Feb 2020 at 18:21, Lei Qian  wrote:

> Dear users,
>
> Could I ask a question on dihedrals func types? Thanks!
>
> I used acpype to convert prmtop file and inpcrd file into gromacs files.
> However, in new generated top file,
> The dihedrals propers func is 3. and The dihedrals impropers func is 1.
>
> These two func types are different from propers func 9 and impropers func
> 4.
> (func type 9 and func type 4 can be found in Gromacs documents).
>
> Could I ask the meaning of func type 3 and func type 1 ?
>
> Thanks!
> Lei
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[gmx-users] New ACPYPE server

[Alan]

Dear community,

Since the original server went down due to hardware obsolescence, we are
now happy to announce that finally the new ACPYPE server is up and running
in a new site hosted at http://bio2byte.be/

http://bio2byte.com/acpype/

If you used it the past, then you'll need to register again.

If don't know what ACPYPE is but you're a looking for a way to speed up the
process of generating topologies for unusual small molecules like
inhibitors, ligands or drugs? Then check it out.

If having issues, please don't hesitate to let us know.

Thanks!

Alan, Luciano Kagami & Wim Vranken
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Re: [gmx-users] acpype error

[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
>
>
>
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Re: [gmx-users] About 2019 GMX manual

[Alan]

Dear Benson and Paul,

Thank you both very much. I will open the issue in redmine and, Benson, I'd
appreciate if you could act on my behalf at gerrit.

Best regards,

Alan

On Mon, 8 Jul 2019 at 03:37, Paul bauer  wrote:

> Hello,
>
> as Benson said, please open an issue at redmine.gromacs.org for all
> kinds of bugs that you find :) (even documentation issues like this)!
> After this, you can upload a fix for the issue yourself at
> gerrit.gromacs.org after creating an account there, or one of us will
> get around to do this.
>
> Cheers
>
> Paul
>
> On 07/07/2019 19:59, Benson Muite wrote:
> > Hi Alan,
> >
> > This requires making a small change in the git repository at
> > https://gerrit.gromacs.org
> >
> > The relevant line is also mirrored at:
> >
> >
> https://github.com/gromacs/gromacs/blob/master/docs/user-guide/system-preparation.rst
> >
> >
> > but changes typically go through the git repository at
> > gerrit.gromacs.org as indicated at:
> >
> >
> http://manual.gromacs.org/documentation/current/dev-manual/overview.html#documentation-organization
> >
> >
> > Can make the change on your behalf if it would be helpful.
> >
> > Benson
> >
> > On 7/7/19 8:35 PM, Alan wrote:
> >
> >> Is there a better way to report issues with the current manual?
> >>
> >> It's a very minor one, to update a link about ACPYPE on page 25.
> >>
> >> To use: https://github.com/alanwilter/acpype
> >>
> >> Thanks,
> >>
> >> Alan
>
>
> --
> Paul Bauer, PhD
> GROMACS Release Manager
> KTH Stockholm, SciLifeLab
> 0046737308594
>
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[gmx-users] About 2019 GMX manual

[Alan]

Is there a better way to report issues with the current manual?

It's a very minor one, to update a link about ACPYPE on page 25.

To use: https://github.com/alanwilter/acpype

Thanks,

Alan
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[gmx-users] Spatially resolved diffusion coefficient

[Jacob Alan Spooner]

Dear GROMACS users,

I am interested in obtaining a spatially resolved diffusion coefficient for 
water in a confined pore system consisting of a slab of metal and water.  My 
goal is to obtain the xy component of diffusion coefficient (parallel to the 
metal slab) as a function of distance away from the metal (z).  I am familiar 
with the ability to calculate D from the msd or the velocity acf in gromacs, 
but have never been interested in spatial dependence of D. A brief dive into 
the literature shows me that there are several methods for obtaining a distance 
dependent D from MD trajectories and these methods vary widely in complexity.  
I am wondering if anybody has any experience/success with this type of 
calculation using GROMACS and could give some advice regarding the most useful 
tools/methods.

Best Wishes,
Jake Spooner
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Re: [gmx-users] ACPYPE not working.

[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.
> > > > &g

Re: [gmx-users] ACPYPE not working.

[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 se

Re: [gmx-users] ACPYPE not working.

[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!
> >
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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> --
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>
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whole Britain!)
for a charity, would you consider​ ​supporting my​ cause?
http://uk.virginmoneygiving.com/AlanSilva
--
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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 not working.

[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!)
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--
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Senior Bioinformatician, UniProt
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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

[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.
> > > > > > > >>
> > &g

Re: [gmx-users] acpype

[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
> > > > > >> > >
&g

Re: [gmx-users] acpype

[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)
> > > >> > > <http://sites.pharmacy.manchester.ac.uk/bryce/amber> to the
> > format
> > > >> that
> > > >> > > GROMACS is compatible with in .rtp files*. so referred to
> GROMACS
> > > >> > tutorial
> > > >> > > protein-ligand complex and downloaded acpype. installed it using
> > its
> > > >> > > readme.txt file but whenever i typed../acpype.py -i FFF.pdb
> >  At
> > > >> > folder
> > > >> > > *acpype/test*   (/Downloads/acpype-master/acpype) or
> > > >> > > (/Downloads/acpype-master/acpype/test) faced to this error:*
> > > >> > >
> > > >> > >
> > > >> > > *bash: ../acpype.py: No such file or directory*
> > > >> > >
> > > >> > > *while when I typed whereis acpype in terminal , the operating
> > > system
> > > >> > says
> > > >> > > :*
> > > >> > >
> > > >> > >
> > > >> > > *acpype: /usr/local/bin/acpype*
> > > >> > > * it means there is the executable file of acpype . so how come
> I
> > > type
> > > >> > > ../acpype.py -h or ../acpype -i FFF.pdb , the 

Re: [gmx-users] acpype

[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)
> >> > > <http://sites.pharmacy.manchester.ac.uk/bryce/amber> to the format
> >> that
> >> > > GROMACS is compatible with in .rtp files*. so referred to GROMACS
> >> > tutorial
> >> > > protein-ligand complex and downloaded acpype. installed it using its
> >> > > readme.txt file but whenever i typed../acpype.py -i FFF.pdb   At
> >> > folder
> >> > > *acpype/test*   (/Downloads/acpype-master/acpype) or
> >> > > (/Downloads/acpype-master/acpype/test) faced to this error:*
> >> > >
> >> > >
> >> > > *bash: ../acpype.py: No such file or directory*
> >> > >
> >> > > *while when I typed whereis acpype in terminal , the operating
> system
> >> > says
> >> > > :*
> >> > >
> >> > >
> >> > > *acpype: /usr/local/bin/acpype*
> >> > > * it means there is the executable file of acpype . so how come I
> type
> >> > > ../acpype.py -h or ../acpype -i FFF.pdb , the system says NO such
> >> file or
> >> > > directory?*
> >> > > *Is there anyone who ca help me?*
> >> > > *I really would be appreciated it if one help me to solve this and
> can
> >> > > convert the AMBER format files to GRMACS format files.*
> >> > >
> >> > > *best regards*
> >> > > *Farial*
> >> > > --
> >> > > Gromacs Users mailing list
> >> > >
> >> > > * Please search the archive at
> >> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> > > posting!
> >> > >
> >> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> > >
> >> > > * For (un)subscribe requests visit
> >> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> >> > > send a mail to gmx-users-requ...@gromacs.org.
> >> > >
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at
> >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> > posting!
> >> >
> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>

Re: [gmx-users] acpype

[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)
> > <http://sites.pharmacy.manchester.ac.uk/bryce/amber> to the format that
> > GROMACS is compatible with in .rtp files*. so referred to GROMACS
> tutorial
> > protein-ligand complex and downloaded acpype. installed it using its
> > readme.txt file but whenever i typed../acpype.py -i FFF.pdb   At
> folder
> > *acpype/test*   (/Downloads/acpype-master/acpype) or
> > (/Downloads/acpype-master/acpype/test) faced to this error:*
> >
> >
> > *bash: ../acpype.py: No such file or directory*
> >
> > *while when I typed whereis acpype in terminal , the operating system
> says
> > :*
> >
> >
> > *acpype: /usr/local/bin/acpype*
> > * it means there is the executable file of acpype . so how come I type
> > ../acpype.py -h or ../acpype -i FFF.pdb , the system says NO such file or
> > directory?*
> > *Is there anyone who ca help me?*
> > *I really would be appreciated it if one help me to solve this and can
> > convert the AMBER format files to GRMACS format files.*
> >
> > *best regards*
> > *Farial*
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>


-- 
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Re: [gmx-users] acpype

[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)
> <http://sites.pharmacy.manchester.ac.uk/bryce/amber> to the format that
> GROMACS is compatible with in .rtp files*. so referred to GROMACS tutorial
> protein-ligand complex and downloaded acpype. installed it using its
> readme.txt file but whenever i typed../acpype.py -i FFF.pdb   At folder
> *acpype/test*   (/Downloads/acpype-master/acpype) or
> (/Downloads/acpype-master/acpype/test) faced to this error:*
>
>
> *bash: ../acpype.py: No such file or directory*
>
> *while when I typed whereis acpype in terminal , the operating system says
> :*
>
>
> *acpype: /usr/local/bin/acpype*
> * it means there is the executable file of acpype . so how come I type
> ../acpype.py -h or ../acpype -i FFF.pdb , the system says NO such file or
> directory?*
> *Is there anyone who ca help me?*
> *I really would be appreciated it if one help me to solve this and can
> convert the AMBER format files to GRMACS format files.*
>
> *best regards*
> *Farial*
> --
> Gromacs Users mailing list
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> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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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
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Re: [gmx-users] Location of latest version of Acpype

[Alan]

Please, see here https://github.com/alanwilter/acpype

And many thanks for using ACPYPE!

Alan

On Tue, 23 Oct 2018 at 21:02, Matthew Fisher 
wrote:

> Dear all,
>
>
> I'm currently trying to locate the latest version of acpype and have been
> unable to find a working link to the script/installer. Could anyone please
> point me in the right direction?
>
>
> Thanks,
>
> Matthew Fisher
> --
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>


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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
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Re: [gmx-users] i have queston about partial charge zinc

[Alan]

The original online server at the University of Cambridge has been retired
after almost 8 years of service I'm sorry. The machine there was really
outdated and impossible to update ACPYPE with new features we've developed
in the past couple of years.

We are working to have the new one up and running but unfortunately I can
predict a date for the return.

For sure, we will announce in the proper channels when the new server is up.

Sorry for the inconvenience,

Alan

On Sun, 30 Sep 2018 at 09:11, neelam wafa  wrote:

> Hi !
> Alan the link for updated acpype you have shared is all about the
> downloadable tool. Can you please share the link for online server for
> it. and is their any tutorial to explain the changed protocol.
> looking forward for your cooperation.
>
> Regards
>
> On 9/20/18, Alan  wrote:
> > Please, official, original, updated ACPYPE is now here:
> > https://github.com/alanwilter/acpype
> >
> > Alan
> >
> > On 20 September 2018 at 13:56, Andrea Coletta  >
> > wrote:
> >
> >> In general I would say that +2 is not a good choice, since it seems to
> me
> >> that this is a Zinc complex.
> >>
> >> You may want to look at this:
> >>
> >> http://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm
> >>
> >> you should be able to create the topology in ambertools and then convert
> >> it to gromac with acpype (https://github.com/llazzaro/acpype)
> >>
> >> -Original Message-
> >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of milad
> >> bagheri
> >> Sent: 20. september 2018 14:28
> >> To: gromacs.org_gmx-users@maillist.sys.kth.se
> >> Subject: [gmx-users] i have queston about partial charge zinc
> >>
> >> Hi
> >> I gonna MD simulation a protein that contained a zinc ion for build
> >> topology I used from the amber99sb  force field Atomic charge is written
> >> "+2" in topology.
> >> I wanted to ask if this charge is correct or should be calculated in a
> >> different way?
> >> "PDB id 4row"
> >> sincerely
> >> --
> >> 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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> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
> >
> >
> > --
> > I'll cycle across Britain in 2018 for a charity, would you consider
> > supporting my cause? http://uk.virginmoneygiving.com/AlanSilva
> > Many thanks!
> > --
> > 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!
> >
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> send a
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> >
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>
> * Please search the archive at
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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] i have queston about partial charge zinc

[Alan]

Please, official, original, updated ACPYPE is now here:
https://github.com/alanwilter/acpype

Alan

On 20 September 2018 at 13:56, Andrea Coletta 
wrote:

> In general I would say that +2 is not a good choice, since it seems to me
> that this is a Zinc complex.
>
> You may want to look at this:
>
> http://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm
>
> you should be able to create the topology in ambertools and then convert
> it to gromac with acpype (https://github.com/llazzaro/acpype)
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of milad
> bagheri
> Sent: 20. september 2018 14:28
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] i have queston about partial charge zinc
>
> Hi
> I gonna MD simulation a protein that contained a zinc ion for build
> topology I used from the amber99sb  force field Atomic charge is written
> "+2" in topology.
> I wanted to ask if this charge is correct or should be calculated in a
> different way?
> "PDB id 4row"
> sincerely
> --
> 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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>
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
I'll cycle across Britain in 2018 for a charity, would you consider
supporting my cause? http://uk.virginmoneygiving.com/AlanSilva
Many thanks!
--
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] Output forces only for select group of atoms

[Jacob Alan Spooner]

Thanks Justin.  This is what I expected but I wanted to make sure I had no 
other options before I started trying to mess with the code (not one of my 
strengths).

Cheers,
Jake

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul 
[jalem...@vt.edu]
Sent: Tuesday, February 27, 2018 3:18 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Output forces only for select group of atoms

On 2/27/18 6:16 PM, Jacob Alan Spooner wrote:
> Hi Mark,
>
> Thank you for your speedy reply.  Unfortunately I do not think a rerun will 
> solve my problem since in that case I will just have to output coordinates of 
> the entire system at my desired output frequency for the forces, and will 
> still be generating huge trajectory files.  Ideally I would be outputting the 
> coordinates of the entire system very very infrequently (since I am not 
> really interested in the coordinates), and outputting the forces for a small 
> group of atoms very frequently. So in this case I don't think doing a rerun 
> will save me anyting and will just add a post-processing step. Normally this 
> would not be an issue but I will be running many simulations of these 25 
> atom systems at once, so outputting all the forces (or coordinates) when I 
> only care about a fraction of them will be a significant problem.
>
> If anybody else has any ideas about how I could get around this issue I would 
> be thankful, but I suspect there is no simple solution.

Short of modifying the code, the only option is what Mark suggested.
GROMACS isn't designed to do what you're asking.

-Justin

> Best,
> Jake
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark Abraham 
> [mark.j.abra...@gmail.com]
> Sent: Tuesday, February 27, 2018 1:47 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Output forces only for select group of atoms
>
> Hi,
>
> No, but instead see
> http://manual.gromacs.org/documentation/current/user-guide/mdrun-features.html#re-running-a-simulation
>
> Mark
>
> On Tue, Feb 27, 2018 at 10:28 PM Jacob Alan Spooner <jacob.spoo...@ufv.ca>
> wrote:
>
>> Dear GROMACS users,
>>
>> I am simulating a fairly large system of about 25 atoms and I want to
>> analyze the forces at each output step for only a select group of about 200
>> atoms (and actually only the z component of the force but this is less
>> important).  My question is whether or not there is a simple way to
>> selectively output forces for only my atoms of interest.  I will have long
>> runs and high output frequency so I would really like to avoid having to
>> output force data for the other ~249800 atoms in my system.  Any help is
>> greatly appreciated!
>>
>> Thanks,
>> Jake Spooner
>> --
>> 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.

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Output forces only for select group of atoms

[Jacob Alan Spooner]

Hi Mark,

Thank you for your speedy reply.  Unfortunately I do not think a rerun will 
solve my problem since in that case I will just have to output coordinates of 
the entire system at my desired output frequency for the forces, and will still 
be generating huge trajectory files.  Ideally I would be outputting the 
coordinates of the entire system very very infrequently (since I am not really 
interested in the coordinates), and outputting the forces for a small group of 
atoms very frequently. So in this case I don't think doing a rerun will save me 
anyting and will just add a post-processing step. Normally this would not be an 
issue but I will be running many simulations of these 25 atom systems at 
once, so outputting all the forces (or coordinates) when I only care about a 
fraction of them will be a significant problem.

If anybody else has any ideas about how I could get around this issue I would 
be thankful, but I suspect there is no simple solution.

Best,
Jake
 

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark Abraham 
[mark.j.abra...@gmail.com]
Sent: Tuesday, February 27, 2018 1:47 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Output forces only for select group of atoms

Hi,

No, but instead see
http://manual.gromacs.org/documentation/current/user-guide/mdrun-features.html#re-running-a-simulation

Mark

On Tue, Feb 27, 2018 at 10:28 PM Jacob Alan Spooner <jacob.spoo...@ufv.ca>
wrote:

> Dear GROMACS users,
>
> I am simulating a fairly large system of about 25 atoms and I want to
> analyze the forces at each output step for only a select group of about 200
> atoms (and actually only the z component of the force but this is less
> important).  My question is whether or not there is a simple way to
> selectively output forces for only my atoms of interest.  I will have long
> runs and high output frequency so I would really like to avoid having to
> output force data for the other ~249800 atoms in my system.  Any help is
> greatly appreciated!
>
> Thanks,
> Jake Spooner
> --
> 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
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Output forces only for select group of atoms

[Jacob Alan Spooner]

Dear GROMACS users,

I am simulating a fairly large system of about 25 atoms and I want to 
analyze the forces at each output step for only a select group of about 200 
atoms (and actually only the z component of the force but this is less 
important).  My question is whether or not there is a simple way to selectively 
output forces for only my atoms of interest.  I will have long runs and high 
output frequency so I would really like to avoid having to output force data 
for the other ~249800 atoms in my system.  Any help is greatly appreciated!

Thanks,
Jake Spooner
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[gmx-users] Formula for 9-3 wall potential

[Jacob Alan Spooner]

Dear GROMACS users,

I am attempting some simulations using the wall option with the 9-3 potential.  
The manual is very brief on this topic and does not explicitly show the form of 
this potential.  If anybody is familiar enough with using the 9-3 walls, am I 
correct to assume the interaction between a particle and the wall is calulated 
as follows:

U_lj = (2Pi/3) (rho*epsilon*sigma^3) ((2/15)(sigma/z)^9-(sigma/z)^6)

where rho is the wall density and z is distance from particle to the wall.  Any 
help is greatly appreciated.

Thanks,
Jake Spooner
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Re: [gmx-users] Conversion Amber to Gromacs

[Alan]

Please, get it here

svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
stable/ccpn/python/acpype acpype

Interestingly, but Google code still holds the correct information too:

https://code.google.com/archive/p/acpype/


On 24 October 2017 at 18:34, ABEL Stephane  wrote:

> Hello Elisa,
>
> "J'arrive après la bataille" To be sure that you have correct Amber
> parameters for GROMACS, you could also use the acpype suite*. This suite
> converts  Amber params in gromacs format. The program generates the
> (non)ffbonded.itp and top files in gromacs format from the Amber's LeaP
> tool. It also provides some gromacs and Amber files to perform and a single
> point energy to test if the conversion is correctly done.
>
> I used successfully this code  to convert the Amber lipid14 params for
> POPC lipid in the GROMACS format.
>
> *http://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder
>
> HTH
>
> Stéphane
>
> --
>
> Message: 3
> Date: Tue, 24 Oct 2017 17:17:08 +0200
> From: Elisa Pieri 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Conversion Amber to Gromacs
> Message-ID:
> 

Re: [gmx-users] ligand topology

[Alan]

http://webapps.ccpn.ac.uk/acpype/

On 1 August 2017 at 22:18, Mohammad Zahidul Hossain Khan <
za.par...@gmail.com> wrote:

> Dear Sir
>
> I have just use acpype.py -i OAI.pdb
> I am getting the error:
> ERROR: no 'antechamber' executable!
> ERROR: no 'antechamber' executable... aborting !
> ==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?
> ==> HINT2: is 'antechamber' in your $PATH?
> What 'which antechamber' in your terminal says?
> 'alias' doesn't work for ACPYPE.
> ACPYPE FAILED: 1
> Total time of execution: less than a second
>
> I am thinking that I have to install amber. But I dont want to do that. Is
> there any way that I can create ligand topology for gaff.
>
>
>
> On Tue, Aug 1, 2017 at 11:41 AM, Justin Lemkul <jalem...@vt.edu> wrote:
>
> >
> >
> > On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote:
> >
> >> Ok, you should not mix and match forcefields, ¿but in the case of
> >> AMBER99SB for the protein and gaff for ligand? (TIP3P wáter).
> >>
> >
> > GAFF is compatible with AMBER (by design).  My comments were warning that
> > one should not use AMBER for a protein in concert with GROMOS for a
> ligand.
> >
> > -Justin
> >
> > Best regards.
> >> Lucio Montero.
> >>
> >> Enviado desde Correo para Windows 10
> >>
> >> De: Alan
> >> Enviado: martes, 1 de agosto de 2017 11:01 a. m.
> >> Para: Gromacs
> >> Asunto: Re: [gmx-users] ligand topology
> >>
> >> Please this GitHub link is totally outdated and not linked in any sense
> to
> >> the original authors.
> >>
> >> Get the correct ACPYPE here:
> >>
> >> svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
> >> stable/ccpn/python/acpype acpype
> >>
> >> On 1 August 2017 at 15:00, Suhaib Shekfeh <s.shek...@gmail.com> wrote:
> >>
> >> Actually, GAFF forcefield and amber forcefields are compatible. gaff is
> >>> simply amber ff for small molecules.
> >>> You have to get first amber tools. The last release is amber tools 16
> >>> Get the source code from here :
> >>> http://ambermd.org/AmberTools16-get.html
> >>>
> >>> after installation you can use antechamber for creating the
> >>> small-molecule
> >>> parameters
> >>>
> >>> later, you can use a nice free program called ACEPYP, made to convert
> >>> amber
> >>> parameters to gromacs toplogyget the code from here:
> >>>
> >>> https://github.com/t-/acpype
> >>>
> >>> Regards
> >>>
> >>>
> >>>
> >>> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
> >>> za.par...@gmail.com> wrote:
> >>>
> >>> Dear Sir
> >>>>
> >>>> Thank you very much for your reply. Can you give me any link or
> >>>>
> >>> suggestion
> >>>
> >>>> that i can learn for amber force field for protein and ligand.
> >>>>
> >>>> On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul <jalem...@vt.edu>
> wrote:
> >>>>
> >>>>
> >>>>>
> >>>>> On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
> >>>>>
> >>>>> Dear Sir
> >>>>>>
> >>>>>> I am new for protein-ligand complex. I want amber force field (ff03)
> >>>>>>
> >>>>> for
> >>>
> >>>> my
> >>>>>> protein, tip3p for water model and gaff (General Amber force field)
> >>>>>>
> >>>>> for
> >>>
> >>>> ligand. I do not know how to produce gaff force field from pdb and
> >>>>>>
> >>>>> then
> >>>
> >>>> convert for gromacs topology.
> >>>>>>
> >>>>>> I have tried ff03 with gromos ligand topology and tip3p water model
> >>>>>>
> >>>>>> it gives me the error:
> >>>>>> atomtype OM not found
> >>>>>>
> >>>>>> and when I have tried ff03 with gromos topology and spc water model
> it
> >>>>>> gives me the error like:
> >>>>>> atomtype HW not found.
> >>>>>>
> >>>>>> Can anyone help me about it?
> >>&g

Re: [gmx-users] ligand topology

[Alan]

Please this GitHub link is totally outdated and not linked in any sense to
the original authors.

Get the correct ACPYPE here:

svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
stable/ccpn/python/acpype acpype

On 1 August 2017 at 15:00, Suhaib Shekfeh <s.shek...@gmail.com> wrote:

> Actually, GAFF forcefield and amber forcefields are compatible. gaff is
> simply amber ff for small molecules.
> You have to get first amber tools. The last release is amber tools 16
> Get the source code from here :
> http://ambermd.org/AmberTools16-get.html
>
> after installation you can use antechamber for creating the small-molecule
> parameters
>
> later, you can use a nice free program called ACEPYP, made to convert amber
> parameters to gromacs toplogyget the code from here:
>
> https://github.com/t-/acpype
>
> Regards
>
>
>
> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
> za.par...@gmail.com> wrote:
>
> > Dear Sir
> >
> > Thank you very much for your reply. Can you give me any link or
> suggestion
> > that i can learn for amber force field for protein and ligand.
> >
> > On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> >
> > >
> > >
> > > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
> > >
> > >> Dear Sir
> > >>
> > >> I am new for protein-ligand complex. I want amber force field (ff03)
> for
> > >> my
> > >> protein, tip3p for water model and gaff (General Amber force field)
> for
> > >> ligand. I do not know how to produce gaff force field from pdb and
> then
> > >> convert for gromacs topology.
> > >>
> > >> I have tried ff03 with gromos ligand topology and tip3p water model
> > >>
> > >> it gives me the error:
> > >> atomtype OM not found
> > >>
> > >> and when I have tried ff03 with gromos topology and spc water model it
> > >> gives me the error like:
> > >> atomtype HW not found.
> > >>
> > >> Can anyone help me about it?
> > >>
> > >>
> > > You can't mix and match force fields; it's fundamentally wrong.  You
> need
> > > to develop ligand parameters that are consistent with the parent
> protein
> > > force field.  Various tools exist for different force fields, with
> > varying
> > > degrees of reliability.
> > >
> > > -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
> > >
> > > ==
> > > --
> > > 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.
> > >
> >
> >
> >
> > --
> >
> >
> > *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
> > *Email: khan5...@vandals.uidaho.edu <khan5...@vandals.uidaho.edu>*
> > * Skype: parash.khan2*
> > *Cell: +12085967165*
> > --
> > 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.
> >
>
>
>
> --
> Dr. rer. nat. Suhaib Shekfeh
> PhD in Computational Drug Design and Medicinal Chemistry
> Oleariusstr. 11, Halle (Saale), Germany
> LinkedIn : http://www.linkedin.com/pub/suhaib-shekfeh/b/65a/255
> --
> Gromacs Users mailing list
>
> * Please 

Re: [gmx-users] REGARDING TOPOLOGY FILE

[Alan]

You can do:

svn checkout
http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/stable/ccpn/python/acpype
acpype

On 19 January 2017 at 16:01, liming_52 <liming...@163.com> wrote:

> Hi everyone,
>   since my lab is in China, of which internet can not connect Google, is
> there anyone who can send me the source of acpype script? My email is
> liming...@163.com. Thanks a lot!
>
>
>
>
>
>
> --
>
> With my best wishes,
> Ming Li, PhD
> Chinese Academy of Agricultural Sciences, Beijing, China
> --
> 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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>
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
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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[gmx-users] ACPYPE now works with GAFF2

[Alan]

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] Mass and charge data are missing in [ atomtypes ] section.

[Alan]

But read the GMX manual to understand why it's all fine.

On 12 October 2016 at 13:29, Dd H <ddhe...@gmail.com> wrote:

> Thank you!
>
> On 12 October 2016 at 19:50, Alan <alanwil...@gmail.com> wrote:
>
> > It's all fine.
> >
> > On 12 October 2016 at 12:34, Dd H <ddhe...@gmail.com> wrote:
> >
> > > I use this command:
> > > acpype -p filename.prmtop -x filename.inpcrd
> > >
> > > It generates parameter files for GROMACS and my question is about the
> > .top
> > > file of outputs.
> > >
> > > On 12 October 2016 at 18:22, Alan <alanwil...@gmail.com> wrote:
> > >
> > > > Which acpype command did you specifically used?
> > > >
> > > > acpype may be able to use Antechamber and calculate partial charges.
> > See
> > > > acpype -h
> > > >
> > > > On 12 October 2016 at 09:56, Dd H <ddhe...@gmail.com> wrote:
> > > >
> > > > > Hi everyone,
> > > > > I generated a .top file of a ligand using acpype for MD
> simulations.
> > > > There
> > > > > are some new atom types in [ atomtypes ] section, but the data of
> > mass
> > > > and
> > > > > charge columns of the section are zeros. However they can be found
> in
> > > > the [
> > > > > atoms ] section. Can you tell me if this file is ok for MD
> > simulations?
> > > > > Thank you in advance!
> > > > >
> > > > > Dading Huang
> > > > > --
> > > > > 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.
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > 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!
> > > >
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> > > >
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> > > > 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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> > >
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> > 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
> >
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> >
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> >
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> >
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>
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>



-- 
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] Mass and charge data are missing in [ atomtypes ] section.

[Alan]

It's all fine.

On 12 October 2016 at 12:34, Dd H <ddhe...@gmail.com> wrote:

> I use this command:
> acpype -p filename.prmtop -x filename.inpcrd
>
> It generates parameter files for GROMACS and my question is about the .top
> file of outputs.
>
> On 12 October 2016 at 18:22, Alan <alanwil...@gmail.com> wrote:
>
> > Which acpype command did you specifically used?
> >
> > acpype may be able to use Antechamber and calculate partial charges. See
> > acpype -h
> >
> > On 12 October 2016 at 09:56, Dd H <ddhe...@gmail.com> wrote:
> >
> > > Hi everyone,
> > > I generated a .top file of a ligand using acpype for MD simulations.
> > There
> > > are some new atom types in [ atomtypes ] section, but the data of mass
> > and
> > > charge columns of the section are zeros. However they can be found in
> > the [
> > > atoms ] section. Can you tell me if this file is ok for MD simulations?
> > > Thank you in advance!
> > >
> > > Dading Huang
> > > --
> > > 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.
> > >
> >
> >
> >
> > --
> > 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/
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>
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>



-- 
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] Mass and charge data are missing in [ atomtypes ] section.

[Alan]

Which acpype command did you specifically used?

acpype may be able to use Antechamber and calculate partial charges. See
acpype -h

On 12 October 2016 at 09:56, Dd H <ddhe...@gmail.com> wrote:

> Hi everyone,
> I generated a .top file of a ligand using acpype for MD simulations. There
> are some new atom types in [ atomtypes ] section, but the data of mass and
> charge columns of the section are zeros. However they can be found in the [
> atoms ] section. Can you tell me if this file is ok for MD simulations?
> Thank you in advance!
>
> Dading Huang
> --
> 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.
>



-- 
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] Porting to Gromacs of Parmbsc1

[Alan]

g).
>
> Another approach I followed was to load everything on Amber and export to
> Gromacs with ACPYPE before solvating and adding ions. Then I tried to
> generate the box in gromacs but I got the error "No type SOL defined". So I
> tried to include manually the water model on the topology, but then I get
> errors like "Atom type ow_... not defined".
>
> So at this point I am looking for:
> - Either a way to remove overlapping waters or to understand if they are
> coming from amber or it is an ACPYPE problem.
> - A way to incorporate the ions and solvent in Gromacs while using the
> topology generated with ACPYPE.
> - Or the ParmBSC1 field in gromacs or how to export it to gromacs.
>
> Am new to MD simulations, just started two months ago, so any information
> or
> help I can get I will appreciate it.
>
> Thank you!
>
>
>
> --
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>
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European Bioinformatics Institute (EMBL-EBI)
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Re: [gmx-users] top parameters for pluronic f127

[Alan]

It's too big! It will never work.

Try the following alternatives:
- to use gasteiger charge (and then you get only the topology);
- as you said it's a polymer, take the smallest common unit, join 3 pieces
of it and get the topology/charges for it, use the middle unit to extend
the charge for all internal units of your polymer and the extreme to model
your terminals.

Good luck,

Alan

On 3 June 2016 at 18:37, SAKO MIRZAIE <sako.bioc...@gmail.com> wrote:

> Dear All,
>
> I am trying to convert my mol2 file to amber99sb itp to do MD by
> gromacs. but, when I use ACPYPE software, it run and never finished.
> my mol2 file is pluronic F127 and contains 2500 atoms. this structure
> is a polymer and huge in size. how can I get an itp file for my
> polymer? How can I simulate it in MD by gromacs? do polymers have some
> tricks?
>
> the molecular structure of f127 is: A99B67A99
>
> where
>
> A: ethylene oxide
> B: propylene oxide
>
> best regards,
>
> --
> ***
> sako mirzaie
> PhD in biochemistry
> --
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Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
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[gmx-users] Getting and keeping ACPYPE updated

[Alan]

Hi everyone,

Many thanks for those who helped for, used or are interested in ACPYPE.

Since Google Code is now archived and, at University of Cambridge, it has
moved), the right way to get it now is by:

svn checkout
http://svn.code.sf.net/p/ccpn/code/branches/stable/ccpn/python/acpype acpype

Thanks,

Alan

-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
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Re: [gmx-users] updates about ACPYPE

[Alan]

Hi,

Please use svn checkout
http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/stable/ccpn/python/acpype
 acpype

Google Code will be retired and is not writable anymore.

The latest version is:

ACPYPE: AnteChamber PYthon Parser interfacE v. 2015-11-02 10:03:43Z Rev:
8810 (c) 2015 AWSdS

I am trying to look at the Urey-Bradley potential but I can’t promise
anything.

It should still be compatible with GMX 4 and 5, but now parameters are
generated to GMX 4.5/5 by default. I am not aware of any issue.

Thanks,

Alan


On 22 October 2015 at 02:27, yunshi11 . <yunsh...@gmail.com> wrote:

> Hi Alan,
>
> Is this Rev: 403? And does the --gmx45 still compatible with gromacs5
> (although gromacs says its version 5 is mostly backward compatible with
> version 4)?
>
> On Sat, Aug 30, 2014 at 8:40 PM, Alan <alanwil...@gmail.com> wrote:
>
> > Dear community,
> >
> > Many thinks for all of you who uses ACPYPE and my sincere apologises for
> > those who have been facing issues when running ACPYPE in “amb2gmx” module
> > to convert to Gromacs files with Amber Forcefields 12SB and 14SB.
> >
> > I am aware of this issue for more than a year, since AmberTools13 were
> > released.
> >
> > The problem is simple: Amber new forcefields introduced new atom types
> > whose names start with a digit, and Gromacs does not accept them. The
> > simply solution is to prefix these atom types with any letter.
> >
> > I am really sorry for not doing it straightforward a year ago. Mostly
> lack
> > of time to consider some further implications, mainly how/if Gromacs
> would
> > handle these new FF12SB and FF14SB, which is still an open question.
> >
> > So, for downloading or updating ACPYPE, please have a look at:
> >
> > https://code.google.com/p/acpype/
> >
> > Install anew:
> > svn checkout
> >
> >
> http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/stable/ccpn/python/acpype
> > acpype
> >
> > or simply (for those who already have ACPYPE):
> > svn update
> >
> > Many thanks,
> >
> > Alan
> > --
> > Alan Wilter SOUSA da SILVA, DSc
> > 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!
> >
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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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-- 
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Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
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Re: [gmx-users] Virtual Sites in protein-ligand systems

[Alan]

No, ACPYPE won’t give VS. But if I learn more about, I can try to
implement. No guarantee though.

On 30 October 2015 at 10:11, Joan Clark Nicolas <joan.clar...@gmail.com>
wrote:

> I am trying to run MD calculations using a 5 fs timestep, so I need tu use
> Virtual Sites. The problem is that I generate ligand topology with acpype
> and then I add it to the protein topology, so the VS of the ligand are not
> generated. Maybe there is a way to generate VS for the ligand with acpype?
>
> And, about the [ virtual_sites* ] directive, can you tell me where can I
> read about this? maybe this is the thing I am looking for.
>
> Thank You!
>
>
>
> *Joan Clark i Nicolas*
>
> 2015-10-29 18:18 GMT+00:00 Justin Lemkul <jalem...@vt.edu>:
>
> >
> >
> > On 10/28/15 9:57 AM, Joan Clark Nicolas wrote:
> >
> >> Dear gmx users,
> >> I am trying to run MD calculations on a protein-ligand system using
> >> Virtual
> >> Sites, but as I generate my protein and ligand topologies separately
> (with
> >> pdb2gmx and acpype, respectively), the VS for the ligand are not
> >> generated.
> >>
> >> Does anyone know a way to generate the VS for the ligand without adding
> it
> >> to the force field?
> >>
> >>
> > One can define any [ virtual_sites* ] directive manually in the topology.
> > pdb2gmx can build some types of virtual sites, but you'd have to tell us
> > specifically what it is you're trying to do if you want anything really
> > useful.  Soon I will upload a patch that will make virtual site
> > construction easier, and intrinsic to pdb2gmx.  I just need to find the
> > time to work out the kinks...
> >
> > -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
> >
> > ==
> > --
> > 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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> >
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-- 
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Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
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Re: [gmx-users] A simple em.mdp and md.mdp file for GMX 5.0

[Alan]

Dear Mark, the simple
em.mdp:
integrator   = steep
nsteps   = 500

does not work anymore with GMX 5.1.

  ERROR: The cut-off length is longer than half the shortest box vector or
  longer than the smallest box diagonal element. Increase the box size or
  decrease rlist.

How to make it work again and still keep the em.mdp the smallest, simplest
possible?

Thanks,

Alan

On 27 August 2014 at 17:09, Mark Abraham <mark.j.abra...@gmail.com> wrote:

> You only need the integrator :-) Default for everything else works.
>
> Mark
> On Aug 27, 2014 4:24 PM, "Alan" <alanwil...@gmail.com> wrote:
>
> > Hi there,
> >
> > I need a very simple em.mdp and md.mdp, to simply test my generated GMX
> > files from ACPYPE.
> >
> > It contains just a single small molecule without solvent. I just need to
> > test if the topology file is OK (i.e. if grompp and mdrun will accept
> it),
> > so I used to use these parameters with GMX 4:
> >
> > em.mdp:
> > cpp  = /usr/bin/cpp
> > define   = -DFLEXIBLE
> > integrator   = steep
> > nsteps   = 500
> > constraints  = none
> > emtol= 1000.0
> > emstep   = 0.01
> > nstcomm  = 1
> > ns_type  = simple
> > nstlist  = 0
> > rlist= 0
> > rcoulomb = 0
> > rvdw = 0
> > Tcoupl   = no
> > Pcoupl   = no
> > gen_vel  = no
> > nstxout  = 1
> > pbc  = no
> >
> > md.mdp:
> > cpp  = /usr/bin/cpp
> > define   = ;-DFLEXIBLE
> > integrator   = md
> > nsteps   = 500
> > constraints  = none
> > emtol= 1000.0
> > emstep   = 0.01
> > comm_mode= angular
> > ns_type  = simple
> > nstlist  = 0
> > rlist= 0
> > rcoulomb = 0
> > rvdw = 0
> > Tcoupl   = no
> > Pcoupl   = no
> > gen_vel  = no
> > nstxout  = 1
> > pbc  = no
> >
> > But these parameters won’t work anymore with GMX 5. Can someone suggest
> me
> > the minimum alterations or completely new values so I could run a quick
> EM
> > and MD? And if they were compatible to both GMX 4 and 5 that’d be great.
> >
> > Many thanks in advance,
> >
> > Alan
> >
> >
> > --
> > Alan Wilter SOUSA da SILVA, DSc
> > 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!
> >
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> >
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> > 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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-- 
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
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[gmx-users] The simplest em.mdp file for GMX 5 (and perhaps for 4.5)

[Alan]

Hi there,

I used to have this, just for simple quick test:

cat em.mdp

integrator   = steep
nsteps   = 500

Alas, it does not work anymore with GMX 5.

  ERROR: The cut-off length is longer than half the shortest box vector or
  longer than the smallest box diagonal element. Increase the box size or
  decrease rlist.


And my md.mdp (which I didn’t test yet, and I fear it will likely fail too)
is:

integrator   = md
nsteps   = 1000

If I could keep them working for both GMX 5 and 4.5 that would be great.

Thanks,

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] The simplest em.mdp file for GMX 5 (and perhaps for 4.5)

[Alan]

Thanks Justin,

I forgot to mention but my system is just on small molecule, without
solvent, no box defined in principle. So, basically, I want to see if the
topology is “OK” enough for GMX to not complain, like I used to do, before
doing big things.

Thanks,

Alan

On 27 October 2015 at 12:01, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 10/27/15 7:51 AM, Alan wrote:
>
>> Hi there,
>>
>> I used to have this, just for simple quick test:
>>
>> cat em.mdp
>>
>> integrator   = steep
>> nsteps   = 500
>>
>> Alas, it does not work anymore with GMX 5.
>>
>>ERROR: The cut-off length is longer than half the shortest box vector
>> or
>>longer than the smallest box diagonal element. Increase the box size or
>>decrease rlist.
>>
>>
>> And my md.mdp (which I didn’t test yet, and I fear it will likely fail
>> too)
>> is:
>>
>> integrator   = md
>> nsteps   = 1000
>>
>> If I could keep them working for both GMX 5 and 4.5 that would be great.
>>
>>
> The error is related to the size of the system; the default value of rlist
> hasn't changed recently (or ever?) from 1.0 nm, so it seems that your
> bare-bones .mdp file could selectively fail if the system is small or the
> box is incorrectly assigned.  Perhaps it's something related to the Verlet
> scheme becoming the default since 4.5?  The only thing that should affect
> rlist would be verlet-buffer-tolerance.
>
> -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
>
> ==
> --
> 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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-- 
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] A simple em.mdp and md.mdp file for GMX 5.0

[Alan]

On 27 October 2015 at 14:59, Mark Abraham <mark.j.abra...@gmail.com> wrote:

> 3nm box


Dear Mark, 3nm in gro file sorted my issue. I was pulling my hair putting
10 nm (>5 times the largest vector of my molecule) and it was not working.

Many thanks!

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
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Re: [gmx-users] A simple em.mdp and md.mdp file for GMX 5.0

[Alan]

Thanks Victor,

My system is the simplest you can think. It’s just one molecule, say in
vacum, and I just want to check if the topology is OK for GMX, run a single
point energy calculation. This always used to work, but apparently now that
Verlet is default, it looks like I can’t use my yesteryear approach. So,
which minimum parameters do I have to define to run an EM using
steep-descent with 500 iters?

Alan

On 27 October 2015 at 13:38, Victor Rosas Garcia <rosas.vic...@gmail.com>
wrote:

> As I understand it, this error is not dependent on the mdp file, but on
> your system. Maybe you need to define a larger system.  Of course, you
> could try decreasing rlist, but the value of rlist is usually dependent on
> the force field you are using, so you risk breaking the physics if you
> decrease rlist just to make the simulation work.
>
> Hope this helps
>
> Victor
>
> 2015-10-27 7:02 GMT-06:00 Alan <alanwil...@gmail.com>:
>
> > Dear Mark, the simple
> > em.mdp:
> > integrator   = steep
> > nsteps   = 500
> >
> > does not work anymore with GMX 5.1.
> >
> >   ERROR: The cut-off length is longer than half the shortest box vector
> or
> >   longer than the smallest box diagonal element. Increase the box size or
> >   decrease rlist.
> >
> > How to make it work again and still keep the em.mdp the smallest,
> simplest
> > possible?
> >
> > Thanks,
> >
> > Alan
> >
> > On 27 August 2014 at 17:09, Mark Abraham <mark.j.abra...@gmail.com>
> wrote:
> >
> > > You only need the integrator :-) Default for everything else works.
> > >
> > > Mark
> > > On Aug 27, 2014 4:24 PM, "Alan" <alanwil...@gmail.com> wrote:
> > >
> > > > Hi there,
> > > >
> > > > I need a very simple em.mdp and md.mdp, to simply test my generated
> GMX
> > > > files from ACPYPE.
> > > >
> > > > It contains just a single small molecule without solvent. I just need
> > to
> > > > test if the topology file is OK (i.e. if grompp and mdrun will accept
> > > it),
> > > > so I used to use these parameters with GMX 4:
> > > >
> > > > em.mdp:
> > > > cpp  = /usr/bin/cpp
> > > > define   = -DFLEXIBLE
> > > > integrator   = steep
> > > > nsteps   = 500
> > > > constraints  = none
> > > > emtol= 1000.0
> > > > emstep   = 0.01
> > > > nstcomm  = 1
> > > > ns_type  = simple
> > > > nstlist  = 0
> > > > rlist= 0
> > > > rcoulomb = 0
> > > > rvdw = 0
> > > > Tcoupl   = no
> > > > Pcoupl   = no
> > > > gen_vel  = no
> > > > nstxout  = 1
> > > > pbc  = no
> > > >
> > > > md.mdp:
> > > > cpp  = /usr/bin/cpp
> > > > define   = ;-DFLEXIBLE
> > > > integrator   = md
> > > > nsteps   = 500
> > > > constraints  = none
> > > > emtol= 1000.0
> > > > emstep   = 0.01
> > > > comm_mode= angular
> > > > ns_type  = simple
> > > > nstlist  = 0
> > > > rlist= 0
> > > > rcoulomb = 0
> > > > rvdw = 0
> > > > Tcoupl   = no
> > > > Pcoupl   = no
> > > > gen_vel  = no
> > > > nstxout  = 1
> > > > pbc  = no
> > > >
> > > > But these parameters won’t work anymore with GMX 5. Can someone
> suggest
> > > me
> > > > the minimum alterations or completely new values so I could run a
> quick
> > > EM
> > > > and MD? And if they were compatible to both GMX 4 and 5 that’d be
> > great.
> > > >
> > > > Many thanks in advance,
> > > >
> > > > Alan
> > > >
> > > >
> > > > --
> > > > Alan Wilter SOUSA da SILVA, DSc
> > > > Bioinformatician, UniProt
> > > > European B

Re: [gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters

[Alan]

Hi

Not because I developed ACPYPE, but if I’d like to be the most rigorous as
possible, I’d go with ACPYPE and RED (http://q4md-forcefieldtools.org/).

Alan

On 29 May 2015 at 20:53, Ebert Maximilian m.eb...@umontreal.ca wrote:

 I continued to define good partial charges using the tools suggested. I
 found that the combination of Maestro + ffconv or mktop, ACPYPE and
 antechamber + mktop have all advantages and disadvantages depending on the
 organic molecule.

 for instance for acetone with maestro and mktop i could achieve the same
 topology as virtual chemistry. I next tried to generate a topology for
 iso-propanol. Here ACPYPE charges with the mktop atom types gave the closes
 density to the experimental one. I also tried to calculate the heat
 capacity with Cp and Cv to compare it with the literature. My box is
 2.3x2.3x2.3nm large and has about 150 molecules of the organic solvent.
 After 1ns of NPT i get values which are 5x higher than the literature value
 (gmx energy -f npt.edr -fluct_props -nmol 100). I also tried a box 5x5x5nm
 with over 1000 molecules and got the same result. Any idea why the
 simulation using OPLS AA FF is so far of when it comes to the heat capacity?

 thanks
 max



  On May 28, 2015, at 9:19 AM, Ebert Maximilian m.eb...@umontreal.ca
 wrote:
 
  Thanks Justin and Kalev this brings me already much further. I tried
 ffld_server and it works just fine. However, it is like a black box. I
 can’t really find the documentation on how ffld_server gets the charges. Do
 you know where to find the documentation?
 
  Thanks
 
  On May 28, 2015, at 2:22 AM, Kalev Takkis kalev.tak...@gmail.com
 wrote:
 
  If you're after OPLS topologies for GROMACS then one way to derive them
 is
  via Schrödinger's Maestro (free academics version is sufficient) and
  Andrey Frolov's
  ffconv script (http://frolov-pchem.wikispaces.com/ffconv.py). You can
  create a force field represesentation of a molecule with the former
  (described here http://www.schrodinger.com/kb/809) and then convert it
 to
  GROMACS format with the latter.
 
  All the best,
  Kalev
 
  On 28 May 2015 at 03:37, Mohd Farid Ismail 
 mohd.farid.ism...@yandex.com
  wrote:
 
  You can try R.E.D. Server.  It has more charge models (I don't know
  whether that will help).
 
  Also, IMO, one should target the density and the static dielectric
  constant when it comes to VDW and partial charges.  I saw a recent
 paper
  that might be of interest to you
  http://pubs.acs.org/doi/abs/10.1021/jp3002383
 
  --
  Mohd Farid Ismail
 
 
 
 
  28.05.2015, 05:13, Ebert Maximilian m.eb...@umontreal.ca:
 
  I just finished a 1 ns NPT calculation of a 2.3x2.3x2.3 nm box filled
 with
  acetone (130 molecules). The expected density at 300K is 784.1 kg/m^3.
 For
  the virtual chemistry parameters i calculated 798.6 (close to the
 800.1±0.2
  value on their website) and for the parameter derived as explain in
  previous mail I got 817.0 which seems too high. Does anybody has an
 advice
  how I could improve the derivation of my parameters?
 
  Thank you very much,
 
  max
 
  On May 27, 2015, at 3:25 PM, Ebert Maximilian m.eb...@umontreal.ca
  wrote:
 
  I read more about organic solvents in MD and came to the conclusion
 that
  OPLS is indeed the best way to go. Since I couldn’t really find an
  accessible tutorial how to derive topology files for GROMACS and the FF
  OPLS/AA I will document my progress here. Maybe this is of help for
  somebody in the future. In addition, I would like to ask the community
 to
  help me in case you see problems with my approach. Once I have a good
  protocol I will write a tutorial and make it available online.
 
  To validate my approach I am trying to create a parameter set for
 acetone
  which I found on  http://virtualchemistry.org. To generate the OPLS
  topology I used a tool suggested by many people called mktop in version
  2.2.1. I downloaded the ideal geometry of acetone from Ligand Expo and
  generated a GROMACS topology file using the following command:
 
  mktop_2.2.1.pl -i ACN_ideal.pdb -o acn_topology.top -ff opls -conect
 yes
 
  In order to get the charges for this organic molecule I downloaded the
  most recent amber tools and compiled it. I used the AM1-BCC charge
 model to
  generate charges for acetone using the following instructions in
  antechamber:
 
  antechamber -i ACN_ideal.pdb -fi pdb -o acn.mol2 -fo mol2 -c bcc -s 2
 
  I opened the resulting mol2 file in Chimera to map the atoms to the
 atoms
  in my .top file. The charges calculated by antechamber look reasonable
 and
  are comparable to the validated OPLS topology from virtual chemistry:
 
  virtual chemistry charges
 
  [ atoms ]
  ;   nr   type  resnr residue  atom   cgnr charge   mass
  typeBchargeB  massB
 1  opls_280 1   LIG C 1  0.47
   12.011
 2  opls_135 1   LIG C 2 -0.18
   12.011
 3  opls_135 1   LIG

Re: [gmx-users] gmx rmsdist: rmsmax vs. rmscmax

[Alan Manning]

Hi, thanks for the reply.

I now have another question regarding the the rmsdist tool: I'm confused 
why my rmsmax value seems so small. Right now I am simulating a box of 
water only. I'd like to get a matrix of all the atom-atom distances for 
a single frame in my simulation, so use the following command:


gmx rmsdist -f nvt.trr -s nvt.tpr -mean -nosumh -b 100 -e 100

However, this gives an rmsmax = 0.000345129, which is smaller than a 
water molecule, and Im not sure why.


I'm also curious why I need to supply a topology file if all I want to 
calculate is the interactomic distances. I'm likely misunderstanding 
this tool... Thanks in advance for the help.


Regards,
Alan Manning



On 03/16/15 04:24, Justin Lemkul wrote:



On 3/15/15 6:36 PM, Alan Manning wrote:

Hi

What is the difference between the rmsmax and rmscmax values
written to the
screen when running gmx rmsdist? Thanks.



rmscmax is scaled by dividing by the mean (sc for scaled,
presumably).  See calc_rmsd() in gmx_rmsdist.c

-Justin


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[gmx-users] gmx rmsdist: rmsmax vs. rmscmax

[Alan Manning]

Hi

What is the difference between the rmsmax and rmscmax values written 
to the screen when running gmx rmsdist? Thanks.


Regards,
Alan Manning
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Re: [gmx-users] Writing out the neighbor list

[Alan Manning]

Ah OK. I'll probably implement a neighbor list after the fact from the 
trajectory data itself. Thanks.


On 15-03-09 03:17 PM, Mark Abraham wrote:

Hi,

Not really. gmx mdrun -debug n for sufficiently large n (3?) will print out
the IDs of the i and j clusters that are in the cluster-pair list for its
duration, but of course that's buffered and does not correspond directly to
anything that leads to physics. To get a list of particles that interact at
a given time step, you'd have to hack a C kernel that also dumped the atom
indices of pairs that were actually within the cutoff; very doable for the
single-domain case, but not already done for you.

Mark

On Mon, Mar 9, 2015 at 9:48 PM, Alan Manning mann...@physics.ubc.ca wrote:


Hi

Is it possible to have Gromacs write out the neighbor lists as well as the
trajectories? Thanks.

Regards,
Alan Manning
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Re: [gmx-users] Converting Amber parameters to gromacs parameters

[Alan]

In principle, if you have _prmtop_, _inpcrd_ files, then

acpype -p _prmtop_ -x _inpcrd_ [-d]

should be able to handle any situation, even Amber14.

Alan



On 16 December 2014 at 14:12, Magnus Lundborg magnus.lundb...@scilifelab.se
 wrote:

 Hi,

 Have a look at acpype. That should be able to convert from Amber (not
 Amber14 yet, I think) to Gromacs.

 Regards,

 Magnus


 On 12/16/2014 03:03 PM, Carlos Navarro Retamal wrote:

 Dear gromacs users,
 I found recently some parameters for a thylakoid membrane, but sadly they
 were for the Amber software. Is there a way to transform them into gromacs
 parameters?
 Thanks in advance,
 Carlos
 --
 Carlos Navarro Retamal
 Bioinformatic engineer
 Ph.D(c) in Applied Science, Universidad de Talca, Chile
 Center of Bioinformatics and Molecular Simulations (CBSM)
 Universidad de Talca
 2 Norte 685, Casilla 721, Talca - Chile
 Teléfono: 56-71-201 798,
 Fax: 56-71-201 561
 Email: carlos.navarr...@gmail.com or cnava...@utalca.cl


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Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
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Wellcome Trust Genome Campus
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[gmx-users] updates about ACPYPE

[Alan]

Dear community,

Many thinks for all of you who uses ACPYPE and my sincere apologises for
those who have been facing issues when running ACPYPE in “amb2gmx” module
to convert to Gromacs files with Amber Forcefields 12SB and 14SB.

I am aware of this issue for more than a year, since AmberTools13 were
released.

The problem is simple: Amber new forcefields introduced new atom types
whose names start with a digit, and Gromacs does not accept them. The
simply solution is to prefix these atom types with any letter.

I am really sorry for not doing it straightforward a year ago. Mostly lack
of time to consider some further implications, mainly how/if Gromacs  would
handle these new FF12SB and FF14SB, which is still an open question.

So, for downloading or updating ACPYPE, please have a look at:

https://code.google.com/p/acpype/

Install anew:
svn checkout
http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/stable/ccpn/python/acpype
acpype

or simply (for those who already have ACPYPE):
svn update

Many thanks,

Alan
-- 
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
 United Kingdom
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[gmx-users] A simple em.mdp and md.mdp file for GMX 5.0

[Alan]

Hi there,

I need a very simple em.mdp and md.mdp, to simply test my generated GMX
files from ACPYPE.

It contains just a single small molecule without solvent. I just need to
test if the topology file is OK (i.e. if grompp and mdrun will accept it),
so I used to use these parameters with GMX 4:

em.mdp:
cpp  = /usr/bin/cpp
define   = -DFLEXIBLE
integrator   = steep
nsteps   = 500
constraints  = none
emtol= 1000.0
emstep   = 0.01
nstcomm  = 1
ns_type  = simple
nstlist  = 0
rlist= 0
rcoulomb = 0
rvdw = 0
Tcoupl   = no
Pcoupl   = no
gen_vel  = no
nstxout  = 1
pbc  = no

md.mdp:
cpp  = /usr/bin/cpp
define   = ;-DFLEXIBLE
integrator   = md
nsteps   = 500
constraints  = none
emtol= 1000.0
emstep   = 0.01
comm_mode= angular
ns_type  = simple
nstlist  = 0
rlist= 0
rcoulomb = 0
rvdw = 0
Tcoupl   = no
Pcoupl   = no
gen_vel  = no
nstxout  = 1
pbc  = no

But these parameters won’t work anymore with GMX 5. Can someone suggest me
the minimum alterations or completely new values so I could run a quick EM
and MD? And if they were compatible to both GMX 4 and 5 that’d be great.

Many thanks in advance,

Alan


-- 
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
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Re: [gmx-users] A simple em.mdp and md.mdp file for GMX 5.0

[Alan]

Many thanks Mark!

Alan


On 27 August 2014 18:09, Mark Abraham mark.j.abra...@gmail.com wrote:

 You only need the integrator :-) Default for everything else works.

 Mark
 On Aug 27, 2014 4:24 PM, Alan alanwil...@gmail.com wrote:

  Hi there,
 
  I need a very simple em.mdp and md.mdp, to simply test my generated GMX
  files from ACPYPE.
 
  It contains just a single small molecule without solvent. I just need to
  test if the topology file is OK (i.e. if grompp and mdrun will accept
 it),
  so I used to use these parameters with GMX 4:
 
  em.mdp:
  cpp  = /usr/bin/cpp
  define   = -DFLEXIBLE
  integrator   = steep
  nsteps   = 500
  constraints  = none
  emtol= 1000.0
  emstep   = 0.01
  nstcomm  = 1
  ns_type  = simple
  nstlist  = 0
  rlist= 0
  rcoulomb = 0
  rvdw = 0
  Tcoupl   = no
  Pcoupl   = no
  gen_vel  = no
  nstxout  = 1
  pbc  = no
 
  md.mdp:
  cpp  = /usr/bin/cpp
  define   = ;-DFLEXIBLE
  integrator   = md
  nsteps   = 500
  constraints  = none
  emtol= 1000.0
  emstep   = 0.01
  comm_mode= angular
  ns_type  = simple
  nstlist  = 0
  rlist= 0
  rcoulomb = 0
  rvdw = 0
  Tcoupl   = no
  Pcoupl   = no
  gen_vel  = no
  nstxout  = 1
  pbc  = no
 
  But these parameters won’t work anymore with GMX 5. Can someone suggest
 me
  the minimum alterations or completely new values so I could run a quick
 EM
  and MD? And if they were compatible to both GMX 4 and 5 that’d be great.
 
  Many thanks in advance,
 
  Alan
 
 
  --
  Alan Wilter SOUSA da SILVA, DSc
  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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Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
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Re: [gmx-users] Atomic charges: RESP or AM1-BCC

[Alan]

Dear Oliver, I’d recommend to try http://q4md-forcefieldtools.org/REDS/. If
you did all right, it should  t least confirm your RESP results.

Alan


On 19 May 2014 07:20, Oliver Schillinger o.schillin...@fz-juelich.dewrote:

 Hi everyone,

 I am trying to parametrize a ligand for use with the amber force fields
 (amber99sb-nmr1 in particular: https://research.chemistry.
 ohio-state.edu/bruschweiler/protein-force-field/).
 The ligand is EGCG (http://en.wikipedia.org/wiki/Epigallocatechin_gallate
 ).

 The main focus of our studies are protein ligand interactions. Therefore I
 need to get the charges as right as possible. I computed atomic charges
 with two methods: AM1-BCC with antechamber through acpype and RESP at the
 HF/6-31G* level (according to this protocol: http://www.teokem.lu.se/~ulf/
 Methods/resp.html).

 The problem:
 The two sets of atomic charges are significantly different for carbons and
 oxygens, with larger absolute values for RESP (up to 2 times as large for
 some atoms).
 In the validation paper for AM1-BCC (http://www.ncbi.nlm.nih.gov/
 pubmed/12395429), the AM1-BCC method performs slightly better than RESP
 when compared to HF/6-31G* ESP derived charges. However, when I understood
 it correctly, the ESP method is not robust and for burried atoms (methyl
 carbons, etc.) vastly varying charges can give the same quality of fit.

 My Question:
 Which set of charges should I use?
 RESP follows the  original amber charge generation procedure more closely,
 but that does not necessarily yield more physical results of course.

 Does anyone have a clue or experiences to share?

 Kind regards,
 Oliver


 --
 Oliver Schillinger
 PhD student

 Forschungszentrum Juelich GmbH
 52425 Juelich | Germany

 Building 5.8v, Room 3010
 Phone: 02461-61-9532

 Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
 Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
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-- 
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Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
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Re: [gmx-users] Simulating a 282 atom molecule. How do I split it into parts?

[Alan]

Well, allow me this suggestion. Consider using
http://q4md-forcefieldtools.org/ to get the right charges, then update
these charges in the mol2 file and run acpype with “-c user” option. For a
quick test, you can use “-c gas”, which would give you charges via
gasteiger method.

Alan


On 5 January 2014 22:07, Jonathan Saboury jsab...@gmail.com wrote:

 I have this molecule I want to simulate:
 http://pastebin.com/raw.php?i=7bsWKjU3

 I have tried using acpype on the whole thing to obtain the needed .itp and
 .gro, but it takes a couple days to finish and I get errors because I do
 not have enough memory.

 I was wondering if splitting this molecule into parts, much like how
 proteins are split into amino acid sections, would be a feasible way to
 simulate this molecule. I haven't seen any tutorials on this, so not sure.

 I could split the molecule into the bowl shapes, the n-hexanes, and the
 n-pentane linker. Or if that would not be the correct way, how would you do
 it?

 My question is how would the input sections deal with the bonds between
 sections? For example, if I had a ethane and wanted to split it into two
 methyl pieces, would I make the input .pdb's as CH3's? I.E.:
 http://pastebin.com/raw.php?i=jhwcYbAM

 And more importantly, how would I link these together in the .gro file?
 (assuming it is the .gro file)

 Thank you, your help is very much appreciated!

 -Jonathan
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Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
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United Kingdom
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