Dear Yanmei Song：
I used gromacs version 3.3.1. I update ffG45a3.rtp to include my molecule. When
I run pdb2gmx using my molecules with the command:
"pdb2gmx -f min_C16.pdb -o C16.pdb -p topol.top -ff G45a3"
I got the error message:
" Opening library file ffG45a3.rtp
Opening library file /user/localgromacs/share/gromacs/top/aminoacid.dat
Reading min_C16.pdb...
', 81 atomsin in water
Opening library file /user/localgromacs/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 81 atoms
chain #res #atoms
1 ' ' 1 81
All occupancies are one
Opening library file ffG45a3.atp
Atomtype 49
Reading residue database... (ffG45a3)
Opening library file ffG45a3.rtp
Using default: not generating all posible dihedrals
Using default:excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing impropers on same bond as a proper
-------------------------------------------------------
>>>> Program pdb2gmx, VERSION 3.3.1
>>>> Source code file: resall.c, line: 331
>>>>
>>>> Fatal error:
>>>> in .rtp file at line: "
The molecule I added in the ffG45a3.rtp is in attached file
Thank you very much indeed.
Angel
{\rtf1\ansi\ansicpg936\deff0\deflang1033\deflangfe2052{\fonttbl{\f0\fmodern\fprq6\fcharset134 \'cb\'ce\'cc\'e5;}}
{\*\generator Msftedit 5.41.15.1507;}\viewkind4\uc1\pard\lang2052\f0\fs20 [ DRG2 ]\par
[ atoms ]\par
CCN CH3 0.00000 1\par
CCM CH1 0.08300 2\par
CCO CH3 0.03300 2\par
CCK CH2 0.05000 2\par
CCI CH2 0.08300 2\par
CCJ C 0.23500 2\par
OCL OA -0.10600 2\par
OCT O -0.37800 2\par
NCH NR 0.07300 3\par
HCH H -0.01100 3\par
CCB C 0.22100 3\par
OCD O -0.40200 3\par
CCA CH2 0.07600 3\par
CCC CH2 0.04300 3\par
CCE CH1 0.07500 4\par
CCG CH3 0.02500 4\par
CCF CH3 0.02700 4\par
NBZ NR 0.07200 4\par
HBZ H -0.01100 4\par
CBT C 0.21900 4\par
OBV O -0.40700 4\par
CBS CH2 0.12900 5\par
CBU CH2 0.09200 5\par
CBW C 0.33900 5\par
OBY OM -0.28000 5\par
OBX OM -0.28000 5\par
NBR NR 0.06800 6\par
HBR H -0.01200 6\par
CBM C 0.20900 6\par
OBO O -0.42600 6\par
CBL CH2 0.07000 6\par
CBN CH1 0.07000 6\par
CBQ CH3 0.02100 6\par
CBP CH3 0.01800 7\par
NBK NR 0.06600 7\par
HBK H -0.01200 7\par
CBE C 0.20200 7\par
OBG O -0.44100 7\par
CBD CH2 0.06600 7\par
CBF CH2 0.03500 7\par
CBH CH1 0.06600 7\par
CBJ CH3 0.00000 8\par
CBI CH3 0.01800 9\par
NBC NR 0.06600 9\par
HBC H -0.01200 9\par
C C 0.20200 9\par
O O -0.44100 9\par
CA CH2 0.06600 9\par
CB CH2 0.03500 9\par
CG CH1 0.06600 9\par
CD2 CH3 0.02200 10\par
CD1 CH3 0.02200 10\par
N NR 0.06900 10\par
H H -0.01200 10\par
CAX C 0.21100 10\par
OAY O -0.42200 10\par
CAW CH2 0.07100 10\par
CAV CH2 0.03900 10\par
CAU CH2 0.10900 11\par
CAT C 0.38500 11\par
OBA OM -0.24700 11\par
OAZ OM -0.24700 11\par
NBB NR 0.06300 12\par
HBB H -0.01300 12\par
CAA C 0.19600 12\par
OAG O -0.45500 12\par
CAB CH2 0.03200 12\par
CAC CH1 0.11400 12\par
CAD CH2 0.03100 12\par
CAE CH2 0.03200 12\par
CAF CH2 0.00000 13\par
CAH CH2 0.00000 13\par
CAI CH2 0.00000 13\par
CAJ CH2 0.00000 13\par
CAK CH2 0.00000 13\par
CCP CH2 0.00000 13\par
CCQ CH2 -0.00300 14\par
CCR CH2 -0.00200 14\par
CCS CH1 0.03100 14\par
CCV CH3 -0.02600 14\par
CCU CH3 0.00000 15\par
[ bonds ]\par
CCM CCN 0.1530 7150000.0\par
CCM CCO 0.1530 7150000.0\par
CCM CCK 0.1530 7150000.0\par
CCI CCK 0.1530 7150000.0\par
CCI CCJ 0.1390 8660000.0\par
CCI NCH 0.1480 7640000.0\par
CCJ OCL 0.1360 10200000.0\par
CCJ OCT 0.1230 16600000.0\par
CAC OCL 0.1440 6100000.0\par
NCH HCH 0.1000 18700000.0\par
CCB NCH 0.1400 8540000.0\par
CCB OCD 0.1230 16600000.0\par
CCA CCB 0.1390 8660000.0\par
CCA CCC 0.1530 7150000.0\par
CCA NBZ 0.1480 7640000.0\par
CCE CCC 0.1530 7150000.0\par
CCE CCG 0.1530 7150000.0\par
CCE CCF 0.1530 7150000.0\par
NBZ HBZ 0.1000 18700000.0\par
CBT NBZ 0.1400 8540000.0\par
CBT OBV 0.1230 16600000.0\par
CBS CBT 0.1390 8660000.0\par
CBS CBU 0.1530 7150000.0\par
CBS NBR 0.1480 7640000.0\par
CBW CBU 0.1530 7150000.0\par
CBW OBY 0.1250 13400000.0\par
CBW OBX 0.1250 13400000.0\par
NBR HBR 0.1000 18700000.0\par
CBM NBR 0.1400 8540000.0\par
CBM OBO 0.1230 16600000.0\par
CBL CBM 0.1390 8660000.0\par
CBL CBN 0.1530 7150000.0\par
CBL NBK 0.1480 7640000.0\par
CBN CBQ 0.1530 7150000.0\par
CBN CBP 0.1530 7150000.0\par
NBK HBK 0.1000 18700000.0\par
CBE NBK 0.1400 8540000.0\par
CBE OBG 0.1230 16600000.0\par
CBD CBE 0.1390 8660000.0\par
CBD CBF 0.1530 7150000.0\par
CBD NBC 0.1480 7640000.0\par
CBH CBF 0.1530 7150000.0\par
CBH CBJ 0.1530 7150000.0\par
CBH CBI 0.1530 7150000.0\par
NBC HBC 0.1000 18700000.0\par
C NBC 0.1400 8540000.0\par
C O 0.1230 16600000.0\par
CA C 0.1390 8660000.0\par
CA CB 0.1530 7150000.0\par
CA N 0.1480 7640000.0\par
CG CB 0.1530 7150000.0\par
CG CD2 0.1530 7150000.0\par
CG CD1 0.1530 7150000.0\par
N H 0.1000 18700000.0\par
CAX N 0.1400 8540000.0\par
CAX OAY 0.1230 16600000.0\par
CAW CAX 0.1390 8660000.0\par
CAW CAV 0.1530 7150000.0\par
CAW NBB 0.1480 7640000.0\par
CAV CAU 0.1530 7150000.0\par
CAT CAU 0.1530 7150000.0\par
CAT OBA 0.1250 13400000.0\par
CAT OAZ 0.1250 13400000.0\par
NBB HBB 0.1000 18700000.0\par
CAA NBB 0.1400 8540000.0\par
CAA OAG 0.1230 16600000.0\par
CAA CAB 0.1390 8660000.0\par
CAC CAB 0.1520 5430000.0\par
CAC CAD 0.1530 7150000.0\par
CAD CAE 0.1530 7150000.0\par
CAE CAF 0.1530 7150000.0\par
CAF CAH 0.1530 7150000.0\par
CAH CAI 0.1530 7150000.0\par
CAI CAJ 0.1530 7150000.0\par
CAJ CAK 0.1530 7150000.0\par
CAK CCP 0.1530 7150000.0\par
CCP CCQ 0.1530 7150000.0\par
CCQ CCR 0.1530 7150000.0\par
CCS CCR 0.1530 7150000.0\par
CCS CCV 0.1530 7150000.0\par
CCS CCU 0.1530 7150000.0\par
[ angles ]\par
CCN CCM CCO 109.5 520.0\par
CCN CCM CCK 109.5 520.0\par
CCO CCM CCK 109.5 520.0\par
CCM CCK CCI 109.5 520.0\par
CCK CCI CCJ 109.5 520.0\par
CCK CCI NCH 111.0 530.0\par
CCJ CCI NCH 109.5 447.3\par
CCI CCJ OCL 115.0 610.0\par
CCI CCJ OCT 121.0 685.0\par
OCL CCJ OCT 124.0 730.0\par
CCJ OCL CAC 109.5 380.0\par
CCI NCH HCH 120.0 505.0\par
CCI NCH CCB 120.0 505.0\par
HCH NCH CCB 120.0 505.0\par
NCH CCB OCD 120.0 560.0\par
NCH CCB CCA 120.0 560.0\par
OCD CCB CCA 121.0 685.0\par
CCB CCA CCC 109.5 520.0\par
CCB CCA NBZ 109.5 447.3\par
CCC CCA NBZ 111.0 530.0\par
CCA CCC CCE 109.5 520.0\par
CCC CCE CCG 109.5 520.0\par
CCC CCE CCF 109.5 520.0\par
CCG CCE CCF 109.5 520.0\par
CCA NBZ HBZ 120.0 505.0\par
CCA NBZ CBT 120.0 505.0\par
HBZ NBZ CBT 120.0 505.0\par
NBZ CBT OBV 120.0 560.0\par
NBZ CBT CBS 120.0 560.0\par
OBV CBT CBS 121.0 685.0\par
CBT CBS CBU 109.5 520.0\par
CBT CBS NBR 109.5 447.3\par
CBU CBS NBR 111.0 530.0\par
CBS CBU CBW 109.5 520.0\par
CBU CBW OBY 117.0 635.0\par
CBU CBW OBX 117.0 635.0\par
OBY CBW OBX 126.0 770.0\par
CBS NBR HBR 120.0 505.0\par
CBS NBR CBM 120.0 505.0\par
HBR NBR CBM 120.0 505.0\par
NBR CBM OBO 120.0 560.0\par
NBR CBM CBL 120.0 560.0\par
OBO CBM CBL 121.0 685.0\par
CBM CBL CBN 109.5 520.0\par
CBM CBL NBK 109.5 447.3\par
CBN CBL NBK 111.0 530.0\par
CBL CBN CBQ 109.5 520.0\par
CBL CBN CBP 109.5 520.0\par
CBQ CBN CBP 109.5 520.0\par
CBL NBK HBK 120.0 505.0\par
CBL NBK CBE 120.0 505.0\par
HBK NBK CBE 120.0 505.0\par
NBK CBE OBG 120.0 560.0\par
NBK CBE CBD 120.0 560.0\par
OBG CBE CBD 121.0 685.0\par
CBE CBD CBF 109.5 520.0\par
CBE CBD NBC 109.5 447.3\par
CBF CBD NBC 111.0 530.0\par
CBD CBF CBH 109.5 520.0\par
CBF CBH CBJ 109.5 520.0\par
CBF CBH CBI 109.5 520.0\par
CBJ CBH CBI 109.5 520.0\par
CBD NBC HBC 120.0 505.0\par
CBD NBC C 120.0 505.0\par
HBC NBC C 120.0 505.0\par
NBC C O 120.0 560.0\par
NBC C CA 120.0 560.0\par
O C CA 121.0 685.0\par
C CA CB 109.5 520.0\par
C CA N 109.5 447.3\par
CB CA N 111.0 530.0\par
CA CB CG 109.5 520.0\par
CB CG CD2 109.5 520.0\par
CB CG CD1 109.5 520.0\par
CD2 CG CD1 109.5 520.0\par
CA N H 120.0 505.0\par
CA N CAX 120.0 505.0\par
H N CAX 120.0 505.0\par
N CAX OAY 120.0 560.0\par
N CAX CAW 120.0 560.0\par
OAY CAX CAW 121.0 685.0\par
CAX CAW CAV 109.5 520.0\par
CAX CAW NBB 109.5 447.3\par
CAV CAW NBB 111.0 530.0\par
CAW CAV CAU 109.5 520.0\par
CAV CAU CAT 109.5 520.0\par
CAU CAT OBA 117.0 635.0\par
CAU CAT OAZ 117.0 635.0\par
OBA CAT OAZ 126.0 770.0\par
CAW NBB HBB 120.0 505.0\par
CAW NBB CAA 120.0 505.0\par
HBB NBB CAA 120.0 505.0\par
NBB CAA OAG 120.0 560.0\par
NBB CAA CAB 120.0 560.0\par
OAG CAA CAB 121.0 685.0\par
CAA CAB CAC 109.5 520.0\par
OCL CAC CAB 109.5 520.0\par
OCL CAC CAD 109.5 320.0\par
CAB CAC CAD 109.5 520.0\par
CAC CAD CAE 109.5 520.0\par
CAD CAE CAF 109.5 520.0\par
CAE CAF CAH 109.5 520.0\par
CAF CAH CAI 109.5 520.0\par
CAH CAI CAJ 109.5 520.0\par
CAI CAJ CAK 109.5 520.0\par
CAJ CAK CCP 109.5 520.0\par
CAK CCP CCQ 109.5 520.0\par
CCP CCQ CCR 109.5 520.0\par
CCQ CCR CCS 109.5 520.0\par
CCR CCS CCV 109.5 520.0\par
CCR CCS CCU 109.5 520.0\par
CCV CCS CCU 109.5 520.0\par
[ impropers ]\par
CCM CCN CCK CCO 35.300 334.8\par
CCI CCK CCJ NCH 35.300 334.8\par
CCJ CCI OCL OCT 0.000 167.4\par
NCH CCI CCB HCH 0.000 167.4\par
CCB NCH OCD CCA 0.000 167.4\par
CCA CCB CCC NBZ 35.300 334.8\par
CCE CCC CCG CCF 35.300 334.8\par
NBZ CCA CBT HBZ 0.000 167.4\par
CBT NBZ OBV CBS 0.000 167.4\par
CBS CBT CBU NBR 35.300 334.8\par
CBW CBU OBY OBX 0.000 167.4\par
NBR CBS CBM HBR 0.000 167.4\par
CBM NBR OBO CBL 0.000 167.4\par
CBL CBM NBK CBN 35.300 334.8\par
CBN CBL CBQ CBP 35.300 334.8\par
NBK CBL CBE HBK 0.000 167.4\par
CBE NBK OBG CBD 0.000 167.4\par
CBD CBE CBF NBC 35.300 334.8\par
CBH CBF CBJ CBI 35.300 334.8\par
NBC CBD C HBC 0.000 167.4\par
C NBC O CA 0.000 167.4\par
CA C N CB 35.300 334.8\par
CG CB CD2 CD1 35.300 334.8\par
N CA CAX H 0.000 167.4\par
CAX N OAY CAW 0.000 167.4\par
CAW CAX CAV NBB 35.300 334.8\par
CAT CAU OBA OAZ 0.000 167.4\par
NBB CAW CAA HBB 0.000 167.4\par
CAA NBB OAG CAB 0.000 167.4\par
CAC CAD OCL CAB 35.300 334.8\par
CCS CCR CCV CCU 35.300 334.8\par
[ dihedrals ]\par
CCI CCK CCM CCN 0.000 5.9 3\par
NCH CCI CCK CCM 0.000 5.9 3\par
CCK CCI CCJ OCT 0.000 1.0 6\par
CCK CCI NCH CCB 0.000 1.0 6\par
CCI CCJ OCL CAC 180.000 16.7 2\par
CAD CAC OCL CCJ 0.000 3.8 3\par
CCA CCB NCH CCI 180.000 33.5 2\par
NBZ CCA CCB NCH 0.000 1.0 6\par
CCE CCC CCA CCB 0.000 5.9 3\par
CCB CCA NBZ CBT 0.000 1.0 6\par
CCF CCE CCC CCA 0.000 5.9 3\par
CBS CBT NBZ CCA 180.000 33.5 2\par
NBR CBS CBT NBZ 0.000 1.0 6\par
CBW CBU CBS CBT 0.000 5.9 3\par
CBT CBS NBR CBM 0.000 1.0 6\par
CBS CBU CBW OBX 0.000 1.0 6\par
CBL CBM NBR CBS 180.000 33.5 2\par
NBK CBL CBM NBR 0.000 1.0 6\par
CBP CBN CBL CBM 0.000 5.9 3\par
CBM CBL NBK CBE 0.000 1.0 6\par
CBD CBE NBK CBL 180.000 33.5 2\par
NBC CBD CBE NBK 0.000 1.0 6\par
CBH CBF CBD CBE 0.000 5.9 3\par
CBE CBD NBC C 0.000 1.0 6\par
CBI CBH CBF CBD 0.000 5.9 3\par
CA C NBC CBD 180.000 33.5 2\par
N CA C NBC 0.000 1.0 6\par
CG CB CA C 0.000 5.9 3\par
C CA N CAX 0.000 1.0 6\par
CD1 CG CB CA 0.000 5.9 3\par
CAW CAX N CA 180.000 33.5 2\par
NBB CAW CAX N 0.000 1.0 6\par
CAU CAV CAW CAX 0.000 5.9 3\par
CAX CAW NBB CAA 0.000 1.0 6\par
CAT CAU CAV CAW 0.000 5.9 3\par
CAV CAU CAT OAZ 0.000 1.0 6\par
CAB CAA NBB CAW 180.000 33.5 2\par
CAC CAB CAA NBB 0.000 1.0 6\par
CAD CAC CAB CAA 0.000 5.9 3\par
CAE CAD CAC OCL 0.000 5.9 3\par
CAF CAE CAD CAC 0.000 5.9 3\par
CAH CAF CAE CAD 0.000 5.9 3\par
CAI CAH CAF CAE 0.000 5.9 3\par
CAJ CAI CAH CAF 0.000 5.9 3\par
CAK CAJ CAI CAH 0.000 5.9 3\par
CCP CAK CAJ CAI 0.000 5.9 3\par
CCQ CCP CAK CAJ 0.000 5.9 3\par
CCR CCQ CCP CAK 0.000 5.9 3\par
CCS CCR CCQ CCP 0.000 5.9 3\par
CCU CCS CCR CCQ 0.000 5.9 3\par
\par
}
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