On Thursday 05 October 2006 16:56, [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? > > I would be grateful for any comments.
take a look at http://mccammon.ucsd.edu/ied/ Notes for using GROMACS to analyze AMBER trajectories These notes are of mostly historical interest, now that IED is able to read output from Ptraj. In general it will be easier to analyze AMBER trajectories with Ptraj than with GROMACS. GROMACS can be used to analyze trajectories produced by the SANDER module of AMBER. GROMACS will read the AMBER trajectory if it is renamed to have an extension of .g87 . GROMACS will not read the AMBER prmtop topology file, but you can produce a pdb file to use as the topology file like this ambpdb -p prmtop <prmcrd >topol.pdb There is one problem with using GROMACS to analyze AMBER data: GROMACS assumes coordinates are in nanometers, while AMBER writes them in Angstroms.You can ignore this problem, in which case all your atoms will be ten times further apart than they should be in IED. Since VMD uses distances to determine bonding for PDB files, this means that if you use a PDB topology file, you won't see any bonds. If you use the van der Waals representation (with an increased radius) and remember to divide any distances you measure by 10, this may be acceptable. If you are comfortable with recompiling GROMACS, you can use the following patch so that your distances will be correct and bonds will appear. Note that with this patch, all .g87 files are assumed to be in units of Angstroms, so if you think you may actually need to read a .g87 file in units of nanometers, this may not be a good idea. The following patch should be applied to src/gmxlib/trxio.c --- trxio.c 2002-02-28 02:49:31.000000000 -0800 +++ trxio.c 2003-12-12 17:11:34.000000000 -0800 @@ -453,14 +453,14 @@ /* else eof! */ return FALSE; } - x[i][m]=x0; + x[i][m]=x0 * 0.1; } } if (bReadBox) { for(m=0; (m<DIM); m++) { if (fscanf(status,"%lf",&x0) != 1) return FALSE; - box[m][m]=x0; + box[m][m]=x0 * 0.1; } } return TRUE; It should be also possible to save a multiple pdb file and than read it with gromacs and convert it to gromacs style trajectory. > > Thank you in advance, > > Nadia Vahdati > > J.W.Essex group > University of Southampton > UK. > > > > > > > > > > _______________________________________________ > 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 Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ 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
