namd-l : Topology info - RESidue information for carbon nanotube

From: prateeksha s (prateeksha.s_at_gmail.com)
Date: Sat Dec 15 2007 - 07:25:19 CST

Hi All,

I'm trying to generate a psf file for a carbon nanotube pdb i have. It is a
6,6 carbon nanotube (cnt) . I am using psfgen to generate the psf. my code
for generating psf goes like this:

package require psfgen
psfgen << ENDMOL
topology top_all27_prot_lipid.inp
segment tube {
pdb nano.pdb
first none
last none
}
coordpdb nano.pdb tube
guesscoord
writepsf cnt.psf
writepdb cnt.pdb
ENDMOL

There is no standard residue for cnt in the topology file, so i had to
create my own , which i did by using bond info from a bgf file (can i do
this?) .

The topology info i included in the topology file goes like this:
RESI CNT 0.00
GROUP
ATOM C000 CA 0.00
ATOM C001 CA 0.00
ATOM C002 CA 0.00
ATOM C003 CA 0.00
ATOM C004 CA 0.00
ATOM C005 CA 0.00
ATOM C006 CA 0.00
...
...
ATOM C140 CA 0.00
ATOM C141 CA 0.00
ATOM C142 CA 0.00
ATOM C143 CA 0.00
BOND C001 C002 C024
BOND C002 C001 C003
BOND C003 C002 C004 C026
BOND C004 C003 C005 C029
BOND C005 C004 C006
BOND C006 C005 C007
BOND C007 C006 C008 C030
BOND C008 C007 C009 C033
BOND C009 C008 C010
BOND C010 C009 C011
BOND C011 C010 C012 C034
BOND C012 C011 C013 C037
BOND C013 C012 C014
BOND C014 C013 C015
BOND C015 C014 C016 C038
BOND C016 C015 C017 C041
BOND C017 C016 C018
BOND C018 C017 C019
BOND C019 C018 C020 C042
BOND C020 C019 C021 C045
BOND C021 C020 C022
BOND C022 C021 C023
BOND C023 C022 C024 C046
BOND C024 C001 C023 C025
BOND C025 C024 C026 C048
BOND C026 C003 C025 C027
BOND C027 C026 C028 C050
BOND C028 C027 C029 C053
BOND C029 C004 C028 C030
BOND C030 C007 C029 C031
BOND C031 C030 C032 C054
BOND C032 C031 C033 C057
BOND C033 C008 C032 C034
BOND C034 C011 C033 C035
BOND C035 C034 C036 C058
BOND C036 C035 C037 C061
BOND C037 C012 C036 C038
BOND C038 C015 C037 C039
BOND C039 C038 C040 C062
BOND C040 C039 C041 C065
BOND C041 C016 C040 C042
BOND C042 C019 C041 C043
BOND C043 C042 C044 C066
BOND C044 C043 C045 C069
BOND C045 C020 C044 C046
BOND C046 C023 C045 C047
BOND C047 C046 C048 C070
BOND C048 C025 C047 C049
BOND C049 C048 C050 C072
BOND C050 C027 C049 C051
BOND C051 C050 C052 C074
BOND C052 C051 C053 C077
BOND C053 C028 C052 C054
BOND C054 C031 C053 C055
BOND C055 C054 C056 C078
BOND C056 C055 C057 C081
BOND C057 C032 C056 C058
BOND C058 C035 C057 C059
BOND C059 C058 C060 C082
BOND C060 C059 C061 C085
BOND C061 C036 C060 C062
BOND C062 C039 C061 C063
BOND C063 C062 C064 C086
BOND C064 C063 C065 C089
BOND C065 C040 C064 C066
BOND C066 C043 C065 C067
BOND C067 C066 C068 C090
BOND C068 C067 C069 C093
BOND C069 C044 C068 C070
BOND C070 C047 C069 C071
BOND C071 C070 C072 C094
BOND C072 C049 C071 C073
BOND C073 C072 C074 C096
BOND C074 C051 C073 C075
BOND C075 C074 C076 C098
BOND C076 C075 C077 C101
BOND C077 C052 C076 C078
BOND C078 C055 C077 C079
BOND C079 C078 C080 C102
BOND C080 C079 C081 C105
BOND C081 C056 C080 C082
BOND C082 C059 C081 C083
BOND C083 C082 C084 C106
BOND C084 C083 C085 C109
BOND C085 C060 C084 C086
BOND C086 C063 C085 C087
BOND C087 C086 C088 C110
BOND C088 C087 C089 C113
BOND C089 C064 C088 C090
BOND C090 C067 C089 C091
BOND C091 C090 C092 C114
BOND C092 C091 C093 C117
BOND C093 C068 C092 C094
BOND C094 C071 C093 C095
BOND C095 C094 C096 C118
BOND C096 C073 C095 C097
BOND C097 C096 C098 C120
BOND C098 C075 C097 C099
BOND C099 C098 C100 C122
BOND C100 C099 C101 C125
BOND C101 C076 C100 C102
BOND C102 C079 C101 C103
BOND C103 C102 C104 C126
BOND C104 C103 C105 C129
BOND C105 C080 C104 C106
BOND C106 C083 C105 C107
BOND C107 C106 C108 C130
BOND C108 C107 C109 C133
BOND C109 C084 C108 C110
BOND C110 C087 C109 C111
BOND C111 C110 C112 C134
BOND C112 C111 C113 C137
BOND C113 C088 C112 C114
BOND C114 C091 C113 C115
BOND C115 C114 C116 C138
BOND C116 C115 C117 C141
BOND C117 C092 C116 C118
BOND C118 C095 C117 C119
BOND C119 C118 C120 C142
BOND C120 C097 C119 C121
BOND C121 C120 C122 C144
BOND C122 C099 C121 C123
BOND C123 C122 C124
BOND C124 C123 C125
BOND C125 C100 C124 C126
BOND C126 C103 C125 C127
BOND C127 C126 C128
BOND C128 C127 C129
BOND C129 C104 C128 C130
BOND C130 C107 C129 C131
BOND C131 C130 C132
BOND C132 C131 C133
BOND C133 C108 C132 C134
BOND C134 C111 C133 C135
BOND C135 C134 C136
BOND C136 C135 C137
BOND C137 C112 C136 C138
BOND C138 C115 C137 C139
BOND C139 C138 C140
BOND C140 C139 C141
BOND C141 C116 C140 C142
BOND C142 C119 C141 C143
BOND C143 C142 C144
BOND C144 C121 C143

Your inputs would be great help !!

Thanks and regard,
Prateeksha Satyamoorthy

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