thanks to all so far @anthony i have amberTools, but not the amber MD package. is that enough for my purpose?
@rui acpypi -i ch3cn_210.pdb says: "cannot find template for residue C3N in our library". and indeed, there's no residue C3N in my ffamber99sb.rtp file (and i don't know, how to use it in order to generate my topology or even an rtp file?!) but (@vitaly) editconf does create the gro file which is fine. however, when i use x2top -f ch3cn_210.pdb -ff select -r x2top.rtp and choose ffamber99sb as force field, i get the error message "Library file ffamber99sb.n2t not found in current dir nor in your GMXLIB path". there are n2t files, but not for the amber ff. what have i done wrong? > I did it for other solvent. If you have AMBER is very easy to do. Do > you have AMBER? > > On Wed, May 19, 2010 at 12:15 PM, vedat durmaz <dur...@zib.de> wrote: >> >> hi all together, >> >> this week i'm trying to do some simulations with acetonitrile (AN) as a >> solvent and using ffamber99 as force field. on this website >> >> http://www.pharmacy.manchester.ac.uk/bryce/amber#box >> >> i found a gorgeous little box containing a pretty number of 6-site >> modeled AN molecules, represented by 3 files: >> >> ch3cn_210.pdb >> frcmod.ch3cn >> prep.ch3cn >> >> does anyone have an idea, how to generate .gro/.itp files out of these >> amber files, preferably by pushing a single button of some proper tool?? >> >> i'ld be the happiest guy in world if someone told me the trick! >> >> regards, >> >> vedat >> >> >> -- >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
