Thank you for the comment. Any comment on the missing [ angles ] in ffamber03.rtp which is included in ffG43a1.rtp? May I leave it out when I define a new residue in ffamber03.rtp?
-----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Tuesday, June 19, 2007 4:31 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Format of a Topology File When Using Amber FF inGromacs 한상화 wrote: > Dear Gromacs users, > > > > I have successfully installed Amber FF in Gromacs according to the > instruction by the Pande Group (http://folding.stanford.edu/ffamber/). > > I ran a demo successfully and enjoyed the speed of Gromacs. > > My questions are: > > [Question 1] The topology file produced by pdb2gmx with Amber FF > (ffamber03, for example) looked different from what we used to obtain > with ffG43a1. > > No force constants were assigned in [ bonds ], [ angles ], [ dihedrals > ], etc. > > > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass > typeB chargeB massB > 1 amber99_25 1 DA5 H5T 1 0.4422 1.008 ; > qtot 0.4422 > 2 amber99_43 1 DA5 O5' 2 -0.6318 16 ; > qtot -0.1896 > 3 amber99_11 1 DA5 C5' 3 -0.0069 12.01 ; > qtot -0.1965 > ...... > > [ bonds ] > ; ai aj funct c0 c1 c2 c3 > 1 2 1 > 2 3 1 > 3 4 1 > ...... > > [ pairs ] > ; ai aj funct c0 c1 c2 c3 > 1 4 1 > 1 5 1 > 1 6 1 > ...... > > [ angles ] > ; ai aj ak funct c0 c1 > c2 c3 > 1 2 3 1 > 2 3 4 1 > 2 3 5 1 > .... > > > > [Question 2] In the RTP file of Amber FF, again no force constants were > assigned in [ bonds ], [ dihedrals ], etc., and _[ angles ] was missing_. > > Is it what it’s supposed to be? > > Here is a sample rtp entry of ffamber03.rtp. > > > > [ GLY ] ; HAx atoms assigned new ff03 atom type > [ atoms ] > N amber99_34 -0.374282 1 > H amber99_17 0.253981 2 > CA amber99_11 -0.128844 3 > HA1 amber99_0 0.088859 4 > HA2 amber99_0 0.088859 5 > C amber99_2 0.580584 6 > O amber99_41 -0.509157 7 > [ bonds ] > N H > N CA > CA HA1 > CA HA2 > CA C > C O > -C N > [ dihedrals ] > CA C +N +H backbone_prop_1 > O C +N +H backbone_prop_2 > -C N CA CB backbone_prop_3 > -C N CA C backbone_prop_4 > CA C +N +CA backbone_prop_1 > O C +N +CA backbone_prop_1 > -C N CA HA1 backbone_prop_5 > -C N CA HA2 backbone_prop_5 > HA1 CA C +N backbone_prop_6 > HA2 CA C +N backbone_prop_6 > [ impropers ] > -C CA N H > CA +N C O > > Any comments would be appreciated. all this information is derived from the atomtypes and can be found in ffamberxxxbon.itp -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 [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 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
