Date: Fri, 9 Oct 2015 14:57:40 +0000
Hi,
I'm trying to calculate hydrogen bonds between two residues using the bond command.
Could somebody please tell me what I'm doing wrong. The commands are listed below.
Thanks
Sid
> atominfo :97
#Atom Name #Res Name #Mol Type Charge Mass GBradius El
1577 N 97 TYR 1 N -0.4157 14.0100 1.5500 N
1578 H 97 TYR 1 H 0.2719 1.0080 1.3000 H
1579 CA 97 TYR 1 CX -0.0014 12.0100 1.7000 C
1580 HA 97 TYR 1 H1 0.0876 1.0080 1.3000 H
1581 CB 97 TYR 1 CT -0.0152 12.0100 1.7000 C
1582 HB2 97 TYR 1 HC 0.0295 1.0080 1.3000 H
1583 HB3 97 TYR 1 HC 0.0295 1.0080 1.3000 H
1584 CG 97 TYR 1 CA -0.0011 12.0100 1.7000 C
1585 CD1 97 TYR 1 CA -0.1906 12.0100 1.7000 C
1586 HD1 97 TYR 1 HA 0.1699 1.0080 1.3000 H
1587 CE1 97 TYR 1 CA -0.2341 12.0100 1.7000 C
1588 HE1 97 TYR 1 HA 0.1656 1.0080 1.3000 H
1589 CZ 97 TYR 1 C 0.3226 12.0100 1.7000 C
1590 OH 97 TYR 1 OH -0.5579 16.0000 1.5000 O
1591 HH 97 TYR 1 HO 0.3992 1.0080 0.8000 H
1592 CE2 97 TYR 1 CA -0.2341 12.0100 1.7000 C
1593 HE2 97 TYR 1 HA 0.1656 1.0080 1.3000 H
1594 CD2 97 TYR 1 CA -0.1906 12.0100 1.7000 C
1595 HD2 97 TYR 1 HA 0.1699 1.0080 1.3000 H
1596 C 97 TYR 1 C 0.5973 12.0100 1.7000 C
1597 O 97 TYR 1 O -0.5679 16.0000 1.5000 O
> atominfo :131
#Atom Name #Res Name #Mol Type Charge Mass GBradius El
2147 N 131 GLN 2 N -0.4157 14.0100 1.5500 N
2148 H 131 GLN 2 H 0.2719 1.0080 1.3000 H
2149 CA 131 GLN 2 CX -0.0031 12.0100 1.7000 C
2150 HA 131 GLN 2 H1 0.0850 1.0080 1.3000 H
2151 CB 131 GLN 2 2C -0.0036 12.0100 1.7000 C
2152 HB2 131 GLN 2 HC 0.0171 1.0080 1.2000 H
2153 HB3 131 GLN 2 HC 0.0171 1.0080 1.2000 H
2154 CG 131 GLN 2 2C -0.0645 12.0100 1.7000 C
2155 HG2 131 GLN 2 HC 0.0352 1.0080 1.2000 H
2156 HG3 131 GLN 2 HC 0.0352 1.0080 1.2000 H
2157 CD 131 GLN 2 C 0.6951 12.0100 1.7000 C
2158 OE1 131 GLN 2 O -0.6086 16.0000 1.5000 O
2159 NE2 131 GLN 2 N -0.9407 14.0100 1.5500 N
2160 HE21 131 GLN 2 H 0.4251 1.0080 1.3000 H
2161 HE22 131 GLN 2 H 0.4251 1.0080 1.3000 H
2162 C 131 GLN 2 C 0.5973 12.0100 1.7000 C
2163 O 131 GLN 2 O -0.5679 16.0000 1.5000 O
> hbond donormask :97 acceptormask:131 out Nhb.dat avgout avdhb.dat
Error: Tokenize: Wrong syntax [a]
HBOND: Donor mask is :97, acceptors will be searched for in region specified by acceptormask:131
Distance cutoff = 3.000, Angle Cutoff = 135.000
Dumping # Hbond v time results to Nhb.dat
Dumping Hbond avgs to avdhb.dat
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