Thank you all for your replies. It has been very helpful. Kind regards
Nadia Quoting Tsjerk Wassenaar <[EMAIL PROTECTED]>: > Hi Nadia, > > Gromacs reads .pdb files (single or multimodel ones) perfectly. The > programmers have noted that .pdb files are in Angstroms usually. > Besides, you don't need an additional .pdb file when reading a .pdb > trajectory (if required you can give the same file as a structure > file). > > Cheers, > > Tsjerk > > On 10/6/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > > > > Hi Mark, > > > > Thank you very much for the clarification. I am also testing this at > the > > moment running with and without Anstroms/nm conversions. > > > > Regards, > > > > Nadia > > > > > > Quoting Mark Abraham <[EMAIL PROTECTED]>: > > > > > [EMAIL PROTECTED] wrote: > > > > Hi gromacs users, > > > > > > > > I am a new user to gromacs and realise that there are lots of > comments > > > on > > > > the archive already about using gromacs with amber outputs but I am > > > getting > > > > rather mixed messages. > > > > > > > > I would like to clarify a few things. I have an Amber trjectory > file > > > saved > > > > through VMD in a .pdb format and a pdb file for the topology. > > > > > > > > I see that some say that one should convert the trajectory file, > some > > > say > > > > that gromacs reads .pdb and others mention changing the extension > to > > > .g87 > > > > and so on. My main question is about the fact that amber works in > > > > Angstroms and gromacs in nm. Should I convert my trajectory.pdb > and > > > > topology.pdb to nm before carrying out principal component > analysis? > > > > > > There would be no need, since PCA is scale-independent. Further, the > PDB > > > format prescribes the use of Angstroms, so I expect any software to > > > presume the use of Angstroms in any PDB file (since they can't tell > the > > > point of origin of the PDB file). You could, of course, test this > > > yourself. > > > > > > Mark > > > _______________________________________________ > > > gmx-users mailing list gmx-users@gromacs.org > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to [EMAIL PROTECTED] > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Groningen Biomolecular Sciences and Biotechnology Institute (GBB) > Dept. of Biophysical Chemistry > University of Groningen > Nijenborgh 4 > 9747AG Groningen, The Netherlands > +31 50 363 4336 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
