Dear Mark:
I used gromacs version 3.3.1. I update ffG45a3.rtp to include my molecule. And
the rtp of my molecule is in the attached file DRG.txt.
Thank you very much!
Angel
[ DRG2 ]
[ atoms ]
CCN CH3 0.00000 1
CCM CH1 0.08300 2
CCO CH3 0.03300 2
CCK CH2 0.05000 2
CCI CH2 0.08300 2
CCJ C 0.23500 2
OCL OA -0.10600 2
OCT O -0.37800 2
NCH NR 0.07300 3
HCH H -0.01100 3
CCB C 0.22100 3
OCD O -0.40200 3
CCA CH2 0.07600 3
CCC CH2 0.04300 3
CCE CH1 0.07500 4
CCG CH3 0.02500 4
CCF CH3 0.02700 4
NBZ NR 0.07200 4
HBZ H -0.01100 4
CBT C 0.21900 4
OBV O -0.40700 4
CBS CH2 0.12900 5
CBU CH2 0.09200 5
CBW C 0.33900 5
OBY OM -0.28000 5
OBX OM -0.28000 5
NBR NR 0.06800 6
HBR H -0.01200 6
CBM C 0.20900 6
OBO O -0.42600 6
CBL CH2 0.07000 6
CBN CH1 0.07000 6
CBQ CH3 0.02100 6
CBP CH3 0.01800 7
NBK NR 0.06600 7
HBK H -0.01200 7
CBE C 0.20200 7
OBG O -0.44100 7
CBD CH2 0.06600 7
CBF CH2 0.03500 7
CBH CH1 0.06600 7
CBJ CH3 0.00000 8
CBI CH3 0.01800 9
NBC NR 0.06600 9
HBC H -0.01200 9
C C 0.20200 9
O O -0.44100 9
CA CH2 0.06600 9
CB CH2 0.03500 9
CG CH1 0.06600 9
CD2 CH3 0.02200 10
CD1 CH3 0.02200 10
N NR 0.06900 10
H H -0.01200 10
CAX C 0.21100 10
OAY O -0.42200 10
CAW CH2 0.07100 10
CAV CH2 0.03900 10
CAU CH2 0.10900 11
CAT C 0.38500 11
OBA OM -0.24700 11
OAZ OM -0.24700 11
NBB NR 0.06300 12
HBB H -0.01300 12
CAA C 0.19600 12
OAG O -0.45500 12
CAB CH2 0.03200 12
CAC CH1 0.11400 12
CAD CH2 0.03100 12
CAE CH2 0.03200 12
CAF CH2 0.00000 13
CAH CH2 0.00000 13
CAI CH2 0.00000 13
CAJ CH2 0.00000 13
CAK CH2 0.00000 13
CCP CH2 0.00000 13
CCQ CH2 -0.00300 14
CCR CH2 -0.00200 14
CCS CH1 0.03100 14
CCV CH3 -0.02600 14
CCU CH3 0.00000 15
[ bonds ]
CCM CCN 0.1530 7150000.0
CCM CCO 0.1530 7150000.0
CCM CCK 0.1530 7150000.0
CCI CCK 0.1530 7150000.0
CCI CCJ 0.1390 8660000.0
CCI NCH 0.1480 7640000.0
CCJ OCL 0.1360 10200000.0
CCJ OCT 0.1230 16600000.0
CAC OCL 0.1440 6100000.0
NCH HCH 0.1000 18700000.0
CCB NCH 0.1400 8540000.0
CCB OCD 0.1230 16600000.0
CCA CCB 0.1390 8660000.0
CCA CCC 0.1530 7150000.0
CCA NBZ 0.1480 7640000.0
CCE CCC 0.1530 7150000.0
CCE CCG 0.1530 7150000.0
CCE CCF 0.1530 7150000.0
NBZ HBZ 0.1000 18700000.0
CBT NBZ 0.1400 8540000.0
CBT OBV 0.1230 16600000.0
CBS CBT 0.1390 8660000.0
CBS CBU 0.1530 7150000.0
CBS NBR 0.1480 7640000.0
CBW CBU 0.1530 7150000.0
CBW OBY 0.1250 13400000.0
CBW OBX 0.1250 13400000.0
NBR HBR 0.1000 18700000.0
CBM NBR 0.1400 8540000.0
CBM OBO 0.1230 16600000.0
CBL CBM 0.1390 8660000.0
CBL CBN 0.1530 7150000.0
CBL NBK 0.1480 7640000.0
CBN CBQ 0.1530 7150000.0
CBN CBP 0.1530 7150000.0
NBK HBK 0.1000 18700000.0
CBE NBK 0.1400 8540000.0
CBE OBG 0.1230 16600000.0
CBD CBE 0.1390 8660000.0
CBD CBF 0.1530 7150000.0
CBD NBC 0.1480 7640000.0
CBH CBF 0.1530 7150000.0
CBH CBJ 0.1530 7150000.0
CBH CBI 0.1530 7150000.0
NBC HBC 0.1000 18700000.0
C NBC 0.1400 8540000.0
C O 0.1230 16600000.0
CA C 0.1390 8660000.0
CA CB 0.1530 7150000.0
CA N 0.1480 7640000.0
CG CB 0.1530 7150000.0
CG CD2 0.1530 7150000.0
CG CD1 0.1530 7150000.0
N H 0.1000 18700000.0
CAX N 0.1400 8540000.0
CAX OAY 0.1230 16600000.0
CAW CAX 0.1390 8660000.0
CAW CAV 0.1530 7150000.0
CAW NBB 0.1480 7640000.0
CAV CAU 0.1530 7150000.0
CAT CAU 0.1530 7150000.0
CAT OBA 0.1250 13400000.0
CAT OAZ 0.1250 13400000.0
NBB HBB 0.1000 18700000.0
CAA NBB 0.1400 8540000.0
CAA OAG 0.1230 16600000.0
CAA CAB 0.1390 8660000.0
CAC CAB 0.1520 5430000.0
CAC CAD 0.1530 7150000.0
CAD CAE 0.1530 7150000.0
CAE CAF 0.1530 7150000.0
CAF CAH 0.1530 7150000.0
CAH CAI 0.1530 7150000.0
CAI CAJ 0.1530 7150000.0
CAJ CAK 0.1530 7150000.0
CAK CCP 0.1530 7150000.0
CCP CCQ 0.1530 7150000.0
CCQ CCR 0.1530 7150000.0
CCS CCR 0.1530 7150000.0
CCS CCV 0.1530 7150000.0
CCS CCU 0.1530 7150000.0
[ angles ]
CCN CCM CCO 109.5 520.0
CCN CCM CCK 109.5 520.0
CCO CCM CCK 109.5 520.0
CCM CCK CCI 109.5 520.0
CCK CCI CCJ 109.5 520.0
CCK CCI NCH 111.0 530.0
CCJ CCI NCH 109.5 447.3
CCI CCJ OCL 115.0 610.0
CCI CCJ OCT 121.0 685.0
OCL CCJ OCT 124.0 730.0
CCJ OCL CAC 109.5 380.0
CCI NCH HCH 120.0 505.0
CCI NCH CCB 120.0 505.0
HCH NCH CCB 120.0 505.0
NCH CCB OCD 120.0 560.0
NCH CCB CCA 120.0 560.0
OCD CCB CCA 121.0 685.0
CCB CCA CCC 109.5 520.0
CCB CCA NBZ 109.5 447.3
CCC CCA NBZ 111.0 530.0
CCA CCC CCE 109.5 520.0
CCC CCE CCG 109.5 520.0
CCC CCE CCF 109.5 520.0
CCG CCE CCF 109.5 520.0
CCA NBZ HBZ 120.0 505.0
CCA NBZ CBT 120.0 505.0
HBZ NBZ CBT 120.0 505.0
NBZ CBT OBV 120.0 560.0
NBZ CBT CBS 120.0 560.0
OBV CBT CBS 121.0 685.0
CBT CBS CBU 109.5 520.0
CBT CBS NBR 109.5 447.3
CBU CBS NBR 111.0 530.0
CBS CBU CBW 109.5 520.0
CBU CBW OBY 117.0 635.0
CBU CBW OBX 117.0 635.0
OBY CBW OBX 126.0 770.0
CBS NBR HBR 120.0 505.0
CBS NBR CBM 120.0 505.0
HBR NBR CBM 120.0 505.0
NBR CBM OBO 120.0 560.0
NBR CBM CBL 120.0 560.0
OBO CBM CBL 121.0 685.0
CBM CBL CBN 109.5 520.0
CBM CBL NBK 109.5 447.3
CBN CBL NBK 111.0 530.0
CBL CBN CBQ 109.5 520.0
CBL CBN CBP 109.5 520.0
CBQ CBN CBP 109.5 520.0
CBL NBK HBK 120.0 505.0
CBL NBK CBE 120.0 505.0
HBK NBK CBE 120.0 505.0
NBK CBE OBG 120.0 560.0
NBK CBE CBD 120.0 560.0
OBG CBE CBD 121.0 685.0
CBE CBD CBF 109.5 520.0
CBE CBD NBC 109.5 447.3
CBF CBD NBC 111.0 530.0
CBD CBF CBH 109.5 520.0
CBF CBH CBJ 109.5 520.0
CBF CBH CBI 109.5 520.0
CBJ CBH CBI 109.5 520.0
CBD NBC HBC 120.0 505.0
CBD NBC C 120.0 505.0
HBC NBC C 120.0 505.0
NBC C O 120.0 560.0
NBC C CA 120.0 560.0
O C CA 121.0 685.0
C CA CB 109.5 520.0
C CA N 109.5 447.3
CB CA N 111.0 530.0
CA CB CG 109.5 520.0
CB CG CD2 109.5 520.0
CB CG CD1 109.5 520.0
CD2 CG CD1 109.5 520.0
CA N H 120.0 505.0
CA N CAX 120.0 505.0
H N CAX 120.0 505.0
N CAX OAY 120.0 560.0
N CAX CAW 120.0 560.0
OAY CAX CAW 121.0 685.0
CAX CAW CAV 109.5 520.0
CAX CAW NBB 109.5 447.3
CAV CAW NBB 111.0 530.0
CAW CAV CAU 109.5 520.0
CAV CAU CAT 109.5 520.0
CAU CAT OBA 117.0 635.0
CAU CAT OAZ 117.0 635.0
OBA CAT OAZ 126.0 770.0
CAW NBB HBB 120.0 505.0
CAW NBB CAA 120.0 505.0
HBB NBB CAA 120.0 505.0
NBB CAA OAG 120.0 560.0
NBB CAA CAB 120.0 560.0
OAG CAA CAB 121.0 685.0
CAA CAB CAC 109.5 520.0
OCL CAC CAB 109.5 520.0
OCL CAC CAD 109.5 320.0
CAB CAC CAD 109.5 520.0
CAC CAD CAE 109.5 520.0
CAD CAE CAF 109.5 520.0
CAE CAF CAH 109.5 520.0
CAF CAH CAI 109.5 520.0
CAH CAI CAJ 109.5 520.0
CAI CAJ CAK 109.5 520.0
CAJ CAK CCP 109.5 520.0
CAK CCP CCQ 109.5 520.0
CCP CCQ CCR 109.5 520.0
CCQ CCR CCS 109.5 520.0
CCR CCS CCV 109.5 520.0
CCR CCS CCU 109.5 520.0
CCV CCS CCU 109.5 520.0
[ impropers ]
CCM CCN CCK CCO 35.300 334.8
CCI CCK CCJ NCH 35.300 334.8
CCJ CCI OCL OCT 0.000 167.4
NCH CCI CCB HCH 0.000 167.4
CCB NCH OCD CCA 0.000 167.4
CCA CCB CCC NBZ 35.300 334.8
CCE CCC CCG CCF 35.300 334.8
NBZ CCA CBT HBZ 0.000 167.4
CBT NBZ OBV CBS 0.000 167.4
CBS CBT CBU NBR 35.300 334.8
CBW CBU OBY OBX 0.000 167.4
NBR CBS CBM HBR 0.000 167.4
CBM NBR OBO CBL 0.000 167.4
CBL CBM NBK CBN 35.300 334.8
CBN CBL CBQ CBP 35.300 334.8
NBK CBL CBE HBK 0.000 167.4
CBE NBK OBG CBD 0.000 167.4
CBD CBE CBF NBC 35.300 334.8
CBH CBF CBJ CBI 35.300 334.8
NBC CBD C HBC 0.000 167.4
C NBC O CA 0.000 167.4
CA C N CB 35.300 334.8
CG CB CD2 CD1 35.300 334.8
N CA CAX H 0.000 167.4
CAX N OAY CAW 0.000 167.4
CAW CAX CAV NBB 35.300 334.8
CAT CAU OBA OAZ 0.000 167.4
NBB CAW CAA HBB 0.000 167.4
CAA NBB OAG CAB 0.000 167.4
CAC CAD OCL CAB 35.300 334.8
CCS CCR CCV CCU 35.300 334.8
[ dihedrals ]
CCI CCK CCM CCN 0.000 5.9 3
NCH CCI CCK CCM 0.000 5.9 3
CCK CCI CCJ OCT 0.000 1.0 6
CCK CCI NCH CCB 0.000 1.0 6
CCI CCJ OCL CAC 180.000 16.7 2
CAD CAC OCL CCJ 0.000 3.8 3
CCA CCB NCH CCI 180.000 33.5 2
NBZ CCA CCB NCH 0.000 1.0 6
CCE CCC CCA CCB 0.000 5.9 3
CCB CCA NBZ CBT 0.000 1.0 6
CCF CCE CCC CCA 0.000 5.9 3
CBS CBT NBZ CCA 180.000 33.5 2
NBR CBS CBT NBZ 0.000 1.0 6
CBW CBU CBS CBT 0.000 5.9 3
CBT CBS NBR CBM 0.000 1.0 6
CBS CBU CBW OBX 0.000 1.0 6
CBL CBM NBR CBS 180.000 33.5 2
NBK CBL CBM NBR 0.000 1.0 6
CBP CBN CBL CBM 0.000 5.9 3
CBM CBL NBK CBE 0.000 1.0 6
CBD CBE NBK CBL 180.000 33.5 2
NBC CBD CBE NBK 0.000 1.0 6
CBH CBF CBD CBE 0.000 5.9 3
CBE CBD NBC C 0.000 1.0 6
CBI CBH CBF CBD 0.000 5.9 3
CA C NBC CBD 180.000 33.5 2
N CA C NBC 0.000 1.0 6
CG CB CA C 0.000 5.9 3
C CA N CAX 0.000 1.0 6
CD1 CG CB CA 0.000 5.9 3
CAW CAX N CA 180.000 33.5 2
NBB CAW CAX N 0.000 1.0 6
CAU CAV CAW CAX 0.000 5.9 3
CAX CAW NBB CAA 0.000 1.0 6
CAT CAU CAV CAW 0.000 5.9 3
CAV CAU CAT OAZ 0.000 1.0 6
CAB CAA NBB CAW 180.000 33.5 2
CAC CAB CAA NBB 0.000 1.0 6
CAD CAC CAB CAA 0.000 5.9 3
CAE CAD CAC OCL 0.000 5.9 3
CAF CAE CAD CAC 0.000 5.9 3
CAH CAF CAE CAD 0.000 5.9 3
CAI CAH CAF CAE 0.000 5.9 3
CAJ CAI CAH CAF 0.000 5.9 3
CAK CAJ CAI CAH 0.000 5.9 3
CCP CAK CAJ CAI 0.000 5.9 3
CCQ CCP CAK CAJ 0.000 5.9 3
CCR CCQ CCP CAK 0.000 5.9 3
CCS CCR CCQ CCP 0.000 5.9 3
CCU CCS CCR CCQ 0.000 5.9 3
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