********> bugfix.34 Author: Randy Radmer Date: 8/16/95 Programs: all_amino94.in, parm94.dat Severity: moderate Problem: Missing parameters and wrong alpha-hydrogen atom type in neutral ASP (ASH) and GLU (GLH). A new residue, negatively-charged cysteine (CYM) is also added by Piotr Cieplak. Affects: Simulations with ASH and GLH residues. Fix: Make the following change to all_amino94.in and 'make db94.dat' ------------------------------------------------------------------------- *** OLD all_amino94.in --- NEW all_amino94.in *************** *** 700,705 CA +M C O DONE CYSTINE(S-S BRIDGE) CYX INT 1 --- 700,733 ----- CA +M C O DONE + CYSTEINE with negative charge + + CYM INT 1 + CORR OMIT DU BEG + 0.00000 + 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 + 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 + 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.73600 + 9 HB1 H1 E 8 6 4 1.090 109.500 60.000 0.24400 + 10 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.24400 + 11 SG SH E 8 6 4 1.810 116.000 180.000 -0.73600 + 12 C C M 6 4 3 1.522 111.100 180.000 0.61600 + 13 O O E 12 6 4 1.229 120.500 0.000 -0.50400 + + CHARGE + -.4157 .2719 -.0351 .0508 -.2413 + .1122 .1122 -.8844 .5973 -.5679 + + IMPROPER + -M CA N HN + CA +M C O + + DONE CYSTINE(S-S BRIDGE) CYX INT 1 *************** *** 820,826 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03410 ! 7 HA HC E 6 4 3 1.090 109.500 300.000 0.08640 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.03160 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.04880 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.04880 --- 848,854 ----- 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03410 ! 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08640 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.03160 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.04880 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.04880 *************** *** 848,854 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 0.01450 ! 7 HA HC E 6 4 3 1.090 109.500 300.000 0.07790 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.00710 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.02560 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.02560 --- 876,882 ----- 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 0.01450 ! 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.07790 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.00710 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.02560 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.02560 ------------------------------------------------------------------------- Fix: Make the following change to parm94.dat ------------------------------------------------------------------------- *** OLD parm94.dat --- NEW parm94.dat *************** *** 147,152 CM-C -O 80.0 125.30 CT-C -O 80.0 120.40 CT-C -O2 70.0 117.00 N*-C -NA 70.0 115.40 N*-C -NC 70.0 118.60 N*-C -O 80.0 120.90 --- 147,153 ----- CM-C -O 80.0 125.30 CT-C -O 80.0 120.40 CT-C -O2 70.0 117.00 + CT-C -OH 70.0 117.00 N*-C -NA 70.0 115.40 N*-C -NC 70.0 118.60 N*-C -O 80.0 120.90 *************** *** 156,161 N -C -O 80.0 122.90 AA general O -C -O 80.0 126.00 AA COO- terminal residues O2-C -O2 80.0 126.00 AA GLU (SCH JPC 79,2379) CA-C -CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes; AA tyr CA-C -OH 70.0 120.00 AA tyr C -CA-CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes --- 157,163 ----- N -C -O 80.0 122.90 AA general O -C -O 80.0 126.00 AA COO- terminal residues O2-C -O2 80.0 126.00 AA GLU (SCH JPC 79,2379) + O -C -OH 80.0 126.00 CA-C -CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes; AA tyr CA-C -OH 70.0 120.00 AA tyr C -CA-CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes *************** *** 430,435 CK-CB-N*-CT 1.0 180. 2. CM-C -N*-CT 1.0 180. 2. dac guess, 9/94 CM-C -CM-CT 1.1 180. 2. NA-CV-CC-CT 1.1 180. 2. NB-CW-CC-CT 1.1 180. 2. NA-CW-CC-CT 1.1 180. 2. --- 432,438 ----- CK-CB-N*-CT 1.0 180. 2. CM-C -N*-CT 1.0 180. 2. dac guess, 9/94 CM-C -CM-CT 1.1 180. 2. + CT-O -C -OH 10.5 180. 2. NA-CV-CC-CT 1.1 180. 2. NB-CW-CC-CT 1.1 180. 2. NA-CW-CC-CT 1.1 180. 2. ------------------------------------------------------------------------- Temporary workarounds: none --