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

2013-01-21 Thread Albert
probably you can try "catdcd" On 01/21/2013 11:29 AM, Anna Marabotti wrote: Dear gmx-users, I followed the suggestions by Justin and Daniel to convert the trajectories, but still Amber does not recognize the correct format and complains about the fact that it does not find the correct box di

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

2013-01-21 Thread Anna Marabotti
Dear gmx-users, I followed the suggestions by Justin and Daniel to convert the trajectories, but still Amber does not recognize the correct format and complains about the fact that it does not find the correct box dimensions. It seems that the two tools are quite incompatible, especially when th

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

2013-01-17 Thread Daniel Larsson
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).

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

2013-01-17 Thread Justin Lemkul
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 trajector

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

2013-01-17 Thread Anna Marabotti
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 complai