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. Sanghwa Han
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