[gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format

Daniel Larsson larsson at xray.bmc.uu.se
Thu Jan 17 13:05:33 CET 2013

On Jan 17, 2013, at 12:27 , Justin Lemkul wrote:

> On 1/17/13 6:22 AM, Anna Marabotti wrote:
>> Dear all,
>> we'd need to convert a trajectory in .xtc format (and the related topology file)
>> to a format that could be read by Amber program (I'd need to perform MM-PBSA
>> calculations).
>> We tried to do it using VMD, but failed to produce a correct trajectory to be
>> read by MMPBSA.py tool. It complains about the fact that it expected only 3 or 6
>> box coords, but I ran the trajectory using a rhombic dodecahedric box, with 9
>> box coords.
>> I read the gmx-user archive to find hints to overcome the problem, but only
>> found incomplete, and in some cases quite old, suggestions (We are currently
>> using Gromacs 4.5.4 version). I don't see anywhere a detailed suggestion on how
>> to proceed, and I have even the doubt that this is not possible to do.
>> Could you please give me some information about, possibly with detailed
>> descriptions about the commands and the flags to use?

The "magic bullet" for converting rhombic dodecahedron box trajectories into something that makes intuitive sense is to use trjconv with the flags -ur compact and -pbc mol. Then trjconv will pick the periodic copy of each molecule that has its mass center the closest to the box center instead of the default of choosing the periodic image that has the mass center inside of the triclinic box.

> You can write a new box using trjconv and make it whatever you want.  Presumably you're stripping out water and such anyway, so all you would have to do is center your solute in whatever box you want:
> -Justin

I agree with Justin. It is probably best to strip of all water and create a new box if amber cannot understand triclinic boxes.

Use the -center or the -fit flag if the solute diffuses out from the original periodic copy of the box. (But be wary to use -fit with operations that rotate the box!) I recommend that you save the original trajectory.


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