From: Jens K. Munk (jkm_at_life.ku.dk)
Date: Sun Oct 23 2011 - 14:39:24 CDT
Dear NAMD-L,
I know this topic has been dealt with previously here, but the previous solutions do not seem to apply to my system. I hope I am not overlooking something obvious.
I am using unnatural amino acids and one of these is 2-amino-3-ethylpentanoic acid, or EPA for short. It is like ILE only the two chains branching out from the beta carbon are both ethyls whereas in ILE they are one ethyl and one methyl.
To make a topology file I extended the methyl group to an ethyl groyp. I made sure to add the new bonds and rename kept atoms appropriately. In the topology file IC table I commented out anything that might contain erroneous information.
I constructed a .pdb by manually "methylating" ILE in a .pdb I have from NMR. I made sure the atom names in the .pdb agreed with those in the topology file. I successfully created .psf.
Now I want to minimize the system in vacuum since this manual editing has probably given rise to suboptimal bonds and angles.
Then comes the mentioned error:
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2 (ATOMS 107 98 100)
These atoms are beta carbon (#98) and the two gamma carbons (#s 107 and 103). This surprises me since I have not done anything to these atoms.
Please help!
File snips:
---
.psf:
94 E 6 EPA N NH1 -0.470000 14.0070 0
95 E 6 EPA HN H 0.310000 1.0080 0
96 E 6 EPA CA CT1 0.070000 12.0110 0
97 E 6 EPA HA HB 0.090000 1.0080 0
98 E 6 EPA CB CT1 -0.090000 12.0110 0
99 E 6 EPA HB HA 0.090000 1.0080 0
100 E 6 EPA CG2 CT2 -0.180000 12.0110 0
101 E 6 EPA HG21 HA 0.090000 1.0080 0
102 E 6 EPA HG22 HA 0.090000 1.0080 0
103 E 6 EPA CD2 CT3 -0.270000 12.0110 0
104 E 6 EPA HD21 HA 0.090000 1.0080 0
105 E 6 EPA HD22 HA 0.090000 1.0080 0
106 E 6 EPA HD23 HA 0.090000 1.0080 0
107 E 6 EPA CG1 CT2 -0.180000 12.0110 0
108 E 6 EPA HG11 HA 0.090000 1.0080 0
109 E 6 EPA HG12 HA 0.090000 1.0080 0
110 E 6 EPA CD1 CT3 -0.270000 12.0110 0
111 E 6 EPA HD11 HA 0.090000 1.0080 0
112 E 6 EPA HD12 HA 0.090000 1.0080 0
113 E 6 EPA HD13 HA 0.090000 1.0080 0
114 E 6 EPA C C 0.510000 12.0110 0
115 E 6 EPA O O -0.510000 15.9990 0
---
.pdb:
ATOM 94 N EPA A 6 10.312 -1.918 1.897 1.00 0.00 E N
ATOM 95 HN EPA A 6 9.341 -1.756 2.060 1.00 0.00 E H
ATOM 96 CA EPA A 6 11.200 -1.097 2.711 1.00 0.00 E C
ATOM 97 HA EPA A 6 11.854 -0.554 2.045 1.00 0.00 E H
ATOM 98 CB EPA A 6 10.410 -0.078 3.553 1.00 0.00 E C
ATOM 99 HB EPA A 6 9.738 -0.622 4.199 1.00 0.00 E H
ATOM 100 CG2 EPA A 6 9.593 0.843 2.644 1.00 0.00 E C
ATOM 101 HG21 EPA A 6 8.928 0.261 2.176 1.00 0.00 E H
ATOM 102 HG22 EPA A 6 10.258 1.340 1.955 1.00 0.00 E H
ATOM 103 CD2 EPA A 6 8.825 1.908 3.396 1.00 0.00 E C
ATOM 104 HD21 EPA A 6 8.487 1.508 4.341 1.00 0.00 E H
ATOM 105 HD22 EPA A 6 9.466 2.758 3.572 1.00 0.00 E H
ATOM 106 HD23 EPA A 6 7.971 2.216 2.811 1.00 0.00 E H
ATOM 107 CG1 EPA A 6 11.355 0.733 4.427 1.00 0.00 E C
ATOM 108 HG11 EPA A 6 11.997 1.235 3.847 1.00 0.00 E H
ATOM 109 HG12 EPA A 6 11.901 0.068 5.079 1.00 0.00 E H
ATOM 110 CD1 EPA A 6 10.542 1.728 5.276 1.00 0.00 E C
ATOM 111 HD11 EPA A 6 9.564 1.302 5.496 1.00 0.00 E H
ATOM 112 HD12 EPA A 6 11.027 1.914 6.131 1.00 0.00 E H
ATOM 113 HD13 EPA A 6 10.429 2.585 4.773 1.00 0.00 E H
ATOM 114 C EPA A 6 12.047 -1.960 3.640 1.00 0.00 E C
ATOM 115 O EPA A 6 13.246 -1.728 3.799 1.00 0.00 E O
---
Topology:
RESI EPA 0.00 !2-amino-3-ethylpentanoic acid, by jkm_at_life.ku.dk
GROUP
ATOM N NH1 -0.47 ! |HG21 HG22 HD21 HD22
ATOM HN H 0.31 ! HN-N \ / | /
ATOM CA CT1 0.07 ! | CG2---CD2--HD23
ATOM HA HB 0.09 ! | /
GROUP ! HA-CA--CB-HB HD11
ATOM CB CT1 -0.09 ! | \ /
ATOM HB HA 0.09 ! | CG1--CD1--HD12
GROUP ! O=C / \ \
ATOM CG2 CT2 -0.18 ! | HG11 HG12 HD13
ATOM HG21 HA 0.09
ATOM HG22 HA 0.09
!ATOM HG23 HA 0.09 ! HG23 removed to change from Ile to Epa, also CG2 charge
GROUP ! changed from -0.27
ATOM CD2 CT3 -0.27 ! Added
ATOM HD21 HA 0.09 ! to
ATOM HD22 HA 0.09 ! make
ATOM HD23 HA 0.09 ! Epa
GROUP
ATOM CG1 CT2 -0.18
ATOM HG11 HA 0.09
ATOM HG12 HA 0.09
GROUP
ATOM CD1 CT3 -0.27
ATOM HD11 HA 0.09
ATOM HD12 HA 0.09
ATOM HD13 HA 0.09
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG1 CB CG2 CB CD1 CG1
BOND N HN N CA C CA C +N
BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21
BOND CG2 HG22 CG2 CD2 CD1 HD11 CD1 HD12 CD1 HD13 !HG23 changed to CD2
BOND CD2 HD21 CD2 HD22 CD2 HD23 !CH3 group added
DOUBLE O C
IMPR N -C CA HN C CA +N O
CMAP -C N CA C N CA C +N
DONOR HN N
ACCEPTOR O C
IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978 !backbone
IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190 !backbone
IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465 !backbone
IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300 !backbone
IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467 !backbone
IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681 !CB rel bb
IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826 !HA rel bb
IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498 !CG1 away from N
IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195 !HB up
IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452 !CG2 down
!IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100 !Removed to
!IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102 !change from
!IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105 !Ile to Epa
IC CA CB CG1 CD1 1.5681 113.6300 180.0000 114.0900 1.5381 !CD1 away from CA
IC CD1 CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130 !HG11 up
IC CD1 CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141 !HG12 down
IC CB CG1 CD1 HD11 1.5498 114.0900 -176.7800 110.3100 1.1115 !\
IC HD11 CG1 *CD1 HD12 1.1115 110.3100 119.7500 110.6500 1.1113 ! |CD1 Hs
IC HD11 CG1 *CD1 HD13 1.1115 110.3100 -119.7000 111.0200 1.1103 !/
--
Venlig hilsen / Kind Regards
M. Sc. Jens K. Munk
Ph.D.-student
Department of Basic Sciences and the Environment
KU-LIFE
Room T432
Phone +45 3533 2429
Thorvaldsensvej 40
DK-1870 Frederiksberg
Denmark
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