getting started with mmtools

[mohammad0325]

Hi,

I am new to mmtools and I want to use it in order to convert topology and coordinate files from amber to gromacs format. Now I don't know how to do it, actually I don’t know how to get started, which file I should download. How can I install it? Can you please help me?

Thank you, Mohammad.

[vvoelz]

Mohammad:

Thanks for the email — I think a better tool for what you describe is the ACPYPE tool. ( http://www.biomedcentral.com/1756-0500/5/367 http://www.biomedcentral.com/1756-0500/5/367 )

If all you want is to convert AMBER structures and topologies to GROMACS, then all you need is a python installation. From the ACPYPE README:

= How To Use ACPYPE =

== Introduction ==

To run acpype with its all functionalities, you need ANTECHAMBER from package
[http://amber.scripps.edu/#AmberTools AmberTools] and
[http://openbabel.org/wiki/Main_Page Open Babel] if your input files are of PDB
format.

However, if one wants acpype just to emulate amb2gmx.pl, one needs nothing
at all but [http://www.python.org Python].

At the moment, acpype is only available for download via svn:

• svn checkout http://acpype.googlecode.com/svn/trunk/ acpype

Yet, if some reason you cannot use svn, one still can get acpype with:

• wget http://acpype.googlecode.com/svn/trunk/acpype.py

But be aware that one may run in extra troubles and I am not willing to support
this way.

Good luck,

Vincent Voelz
voelz@temple.edu

Assistant Professor of Chemistry
Temple University
http://www.voelzlab.org

On Dec 1, 2015, at 12:54 AM, mohammad0325 notifications@github.com wrote:

Hi,

I am new to mmtools and I want to use it in order to convert topology and coordinate files from amber to gromacs format. Now I don't know how to do it, actually I don’t know how to get started, which file I should download. How can I install it? Can you please help me?

Thank you, Mohammad.

—
Reply to this email directly or view it on GitHub #2.

[jchodera]

+1 for ACPYPE being the canonical way to do this.

[mohammad0325]

Thank you all for your help,

I've installed amber tools and the ACPYPE and parmEd for conversion of topology files, but they didn't work good for me, now I'm looking for another program to this conversion for me.

[davidlmobley]

My group has actually moved away from ACPYPE towards ParmEd, which we've worked with Jason Swails to validate against ACPYPE and against energies calculated in AMBER, GROMACS, and OpenMM.

@mohammad0325 - it's worth noting that mmtools isn't really maintained currently and most of the functionality we continue using has moved to github.com/choderalab/openmoltools. BUT, neither mmtools nor openmoltools has an independent converter - they have always relied on one of the other converters (amb2gmx, ACPYPE, ParmEd) for conversion. So you won't find a way to bypass ACPYPE or ParmEd.

I suspect a more profitable line of inquiry for you is to sort out (or explain) WHY ParmEd/ACPYPE don't "work good" for you - i.e., what's wrong with the conversion? It may be a problem with the files you are trying to convert, since these have been used rather extensively for conversion in a number of different groups.

Marking as closed, but reopen if you have further concerns.

[hainm]

@mohammad:

Just curious, you raised the same issue on ParmEd repo before, did you get trouble to make it work?

ParmEd/ParmEd#483

[mohammad0325]

No, I could install and use ParmEd successfully but I don't know why the coordination file looks ok but the topology is not. The bonds are messed when start doing MD. There is something wrong with the internal bonded interactions.

[swails]

No, I could install and use ParmEd successfully but I don't know why the coordination file looks ok but the topology is not. The bonds are messed when start doing MD. There is something wrong with the internal bonded interactions.

As @davidlmobley mentioned, ParmEd and ACPYPE have been validated against each other, and in all of my experiences ParmEd has faithfully converted Amber-style topologies and coordinate files to GROMACS topology and GRO files. This is actually a much easier translation to make than the reverse, since GROMACS supports a superset of AMBER functionality as far as force field functional forms.

So I agree, you should figure out why the conversion does not work rather than trying to find another option to convert. AFAIK, ParmEd and ACPYPE are the only two currently maintained packages that can do this conversion. If neither of those works for you, then most likely nothing out there will.

I actually suspect that the real problem is in your Amber files (i.e., the prmtop does not define what you think it defines). The Amber->Gromacs conversion in ParmEd is most likely working just fine for your system.

[davidlmobley]

Yes, I agree with Jason here. In all likelihood there is a problem with
your system in AMBER.

On Wed, Dec 2, 2015 at 8:37 AM, Jason Swails notifications@github.com
wrote:

No, I could install and use ParmEd successfully but I don't know why the
coordination file looks ok but the topology is not. The bonds are messed
when start doing MD. There is something wrong with the internal bonded
interactions.

As @davidlmobley https://github.com/davidlmobley mentioned, ParmEd and
ACPYPE have been validated against each other, and in all of my experiences
ParmEd has faithfully converted Amber-style topologies and coordinate files
to GROMACS topology and GRO files. This is actually a much easier
translation to make than the reverse, since GROMACS supports a superset of
AMBER functionality as far as force field functional forms.

So I agree, you should figure out why the conversion does not work rather
than trying to find another option to convert. AFAIK, ParmEd and ACPYPE are
the only two currently maintained packages that can do this conversion. If
neither of those works for you, then most likely nothing out there will.

I actually suspect that the real problem is in your Amber files (i.e., the
prmtop does not define what you think it defines). The Amber->Gromacs
conversion in ParmEd is most likely working just fine for your system.

—
Reply to this email directly or view it on GitHub
#2 (comment).

David Mobley
dmobley@gmail.com
949-385-2436

[mohammad0325]

Ok,
Thank you for your answers. I will check my system again.