Re: [gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric), and topologies to Amber format
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 dimensions. It seems that the two tools are quite incompatible, especially when the trajectory is not in the classic cubic format. This is just for records since it is a recurrent query in the gmx-user archive, still apparently with no solution. Many thanks in any case and best regards Anna -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric), and topologies to Amber format
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 the trajectory is not in the classic cubic format. This is just for records since it is a recurrent query in the gmx-user archive, still apparently with no solution. Many thanks in any case and best regards Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 "When a man with a gun meets a man with a pen, the man with the gun is a dead man" (Roberto Benigni, about Roberto Saviano) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format
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. Daniel -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format
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? 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: trjconv -s topol.tpr -f traj.xtc -center -box x y z -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format
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? Many thanks in advance for your kind answer and best regards Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 "When a man with a gun meets a man with a pen, the man with the gun is a dead man" (Roberto Benigni, about Roberto Saviano) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
