Hi Folks, First just want to say thanks to all of those who have responded to my previous questions. I belong to a couple different bb's relating to the various software packages I use, and I have to say this one seems to have the lowest number of unanswered questions (from all users, that is, not just my own).
That said ... I was having problems keeping my histidines planar, and had to manually edit the .top file produced by pdb2gmx in order to fix the problem. I was just wondering if this problem (i.e. incorrect and incomplete improper dihedral records in the top file) is isolated to histidine topologies generated by pdb2gmx using the G53a6 ff parameters or if manual intervention is frequently required for such standard geometries. I'm using Gromacs v3.3. I start with a pdb file of an extended peptide (with planar his) and issue: pdb2gmx -f -ignh -inter 1STN.pdb -o 1STN.gro -p 1STN.top -ff G53a6 whereupon I specify the single histidine to be of type HISB. After: this is what it looks like (converted to pdb format for those interested in a quick glance): ATOM 25 N HIS 3 22.060 19.320 33.570 1.00 0.00 ATOM 26 H HIS 3 21.370 20.040 33.460 1.00 0.00 ATOM 27 CA HIS 3 23.420 19.460 33.060 1.00 0.00 ATOM 28 CB HIS 3 23.470 19.070 31.580 1.00 0.00 ATOM 29 CG HIS 3 24.840 18.510 31.250 1.00 0.00 ATOM 30 ND1 HIS 3 25.830 19.200 30.650 1.00 0.00 ATOM 31 CD2 HIS 3 25.290 17.220 31.540 1.00 0.00 ATOM 32 HD2 HIS 3 24.770 16.500 31.980 1.00 0.00 ATOM 33 CE1 HIS 3 26.900 18.350 30.550 1.00 0.00 ATOM 34 HE1 HIS 3 27.790 18.580 30.140 1.00 0.00 ATOM 35 NE2 HIS 3 26.570 17.140 31.100 1.00 0.00 ATOM 36 HE2 HIS 3 27.160 16.340 31.170 1.00 0.00 ATOM 37 C HIS 3 23.940 20.870 33.230 1.00 0.00 ...planar... and in the topolgy file: (atom records) 25 N 3 HISB N 11 -0.31 14.0067 ; qtot 1.69 26 H 3 HISB H 11 0.31 1.008 ; qtot 2 27 CH1 3 HISB CA 12 0 13.019 ; qtot 2 28 CH2 3 HISB CB 12 0 14.027 ; qtot 2 29 C 3 HISB CG 13 0 12.011 ; qtot 2 30 NR 3 HISB ND1 13 -0.54 14.0067 ; qtot 1.46 31 C 3 HISB CD2 13 0 12.011 ; qtot 1.46 32 HC 3 HISB HD2 13 0.14 1.008 ; qtot 1.6 33 C 3 HISB CE1 13 0 12.011 ; qtot 1.6 34 HC 3 HISB HE1 13 0.14 1.008 ; qtot 1.74 35 NR 3 HISB NE2 13 -0.05 14.0067 ; qtot 1.69 36 H 3 HISB HE2 13 0.31 1.008 ; qtot 2 37 C 3 HISB C 14 0.45 12.011 ; qtot 2.45 38 O 3 HISB O 14 -0.45 15.9994 ; qtot 2 (pertinent dihedral records) 28 31 30 29 2 gi_1 29 31 35 33 2 gi_1 29 30 33 35 2 gi_1 30 33 35 31 2 gi_1 30 29 31 35 2 gi_1 31 29 35 32 2 gi_1 31 29 30 33 2 gi_1 32 35 30 33 2 gi_1 35 31 33 36 2 gi_1 After minimization: ATOM 25 N HIS 3 22.140 19.100 33.570 1.00 0.00 ATOM 26 H HIS 3 21.480 19.800 33.290 1.00 0.00 ATOM 27 CA HIS 3 23.500 19.270 33.040 1.00 0.00 ATOM 28 CB HIS 3 23.480 18.830 31.570 1.00 0.00 ATOM 29 CG HIS 3 24.850 18.320 31.130 1.00 0.00 ATOM 30 ND1 HIS 3 25.790 19.040 30.510 1.00 0.00 ATOM 31 CD2 HIS 3 25.350 17.110 31.390 1.00 0.00 ATOM 32 HD2 HIS 3 25.040 16.250 30.750 1.00 0.00 ATOM 33 CE1 HIS 3 26.740 18.130 30.330 1.00 0.00 ATOM 34 HE1 HIS 3 27.570 18.210 29.640 1.00 0.00 ATOM 35 NE2 HIS 3 26.650 17.290 31.350 1.00 0.00 ATOM 36 HE2 HIS 3 27.370 16.850 31.890 1.00 0.00 ATOM 37 C HIS 3 23.990 20.730 33.170 1.00 0.00 ATOM 38 O HIS 3 23.220 21.650 32.900 1.00 0.00 ...puckered... To correct this it was necessary to delete: 32 35 30 33 2 gi_1 (this auto generated improper was largely responsible for the ring puckering - its removal alone caused much of the problem to be corrected) and to add: 34 30 35 33 2 gi_1 (which brough the HE2 hydrogen slightly out of plain back into plain) Is it recommended that I look over every record in the topology file? Is this necessary? Thanks. Tony Anthony A. Armstrong Department of Biophysics and Biophysical Chemistry Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD 21205 410-955-8715 410-955-0637 FAX [EMAIL PROTECTED] _______________________________________________ gmx-users mailing list [email protected] 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
