[gmx-users] adding a new residue into an existing force field?
marzieh dehghan
dehghanmarzieh at gmail.com
Fri Dec 5 08:59:06 CET 2014
Hi
according to the previous email, since I want to keep covalent bond during
the MD using gromacs, you said me, I should add a new residue into an
existing force field
<http://www.gromacs.org/Documentation/Terminology/Force_Fields>, but I have
two questions?
1- based on the gromacs website , I can copy residuetypes.dat and
spcbond.dat in the working directory. is it possible to copy
" amino acid.rtp, aminoacid.hdb, atomtypes.atp" in the working directory?
2- can I use one of the output file of prodrug server (the gromacs
topology) as aminoacid.rtp?
(copy at the end of aminoacid.rtp or it use as an independent file?)
[ moleculetype ]
; Name nrexcl
GLC 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OM 1 UNK OAF 1 -0.322 15.9994
2 P 1 UNK PAE 1 1.063 30.9738
3 OM 1 UNK OAG 1 -0.322 15.9994
4 OM 1 UNK OAH 1 -0.322 15.9994
5 OA 1 UNK OAD 1 -0.097 15.9994
6 CH2 1 UNK CAC 2 -0.044 14.0270
7 C 1 UNK CAB 2 0.184 12.0110
8 OA 1 UNK OAA 2 -0.149 15.9994
9 H 1 UNK HAA 2 -0.013 1.0080
10 C 1 UNK CAI 2 0.184 12.0110
11 OA 1 UNK OAJ 2 -0.149 15.9994
12 H 1 UNK HAJ 2 -0.013 1.0080
13 C 1 UNK CAK 3 0.218 12.0110
14 OA 1 UNK OAL 3 -0.126 15.9994
15 H 1 UNK HAL 3 -0.011 1.0080
16 C 1 UNK CAM 3 0.218 12.0110
17 OA 1 UNK OAN 3 -0.126 15.9994
18 H 1 UNK HAN 3 -0.011 1.0080
19 CH2 1 UNK CAO 3 -0.025 14.0270
20 OA 1 UNK OAP 3 -0.126 15.9994
21 H 1 UNK HAQ 3 -0.011 1.0080
[ bonds ]
; ai aj fu c0, c1, ...
2 1 2 0.148 8600000.0 0.148 8600000.0 ; PAE OAF
2 3 2 0.148 8600000.0 0.148 8600000.0 ; PAE OAG
2 4 2 0.148 8600000.0 0.148 8600000.0 ; PAE OAH
2 5 2 0.161 4840000.0 0.161 4840000.0 ; PAE OAD
6 5 2 0.143 8180000.0 0.143 8180000.0 ; CAC OAD
7 6 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAC
7 8 2 0.136 10200000.0 0.136 10200000.0 ; CAB OAA
7 10 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAI
8 9 2 0.100 15700000.0 0.100 15700000.0 ; OAA HAA
10 11 2 0.136 10200000.0 0.136 10200000.0 ; CAI OAJ
10 13 2 0.153 7150000.0 0.153 7150000.0 ; CAI CAK
11 12 2 0.100 15700000.0 0.100 15700000.0 ; OAJ HAJ
13 14 2 0.136 10200000.0 0.136 10200000.0 ; CAK OAL
13 16 2 0.153 7150000.0 0.153 7150000.0 ; CAK CAM
14 15 2 0.100 15700000.0 0.100 15700000.0 ; OAL HAL
16 17 2 0.136 10200000.0 0.136 10200000.0 ; CAM OAN
16 19 2 0.153 7150000.0 0.153 7150000.0 ; CAM CAO
17 18 2 0.100 15700000.0 0.100 15700000.0 ; OAN HAN
19 20 2 0.143 8180000.0 0.143 8180000.0 ; CAO OAP
20 21 2 0.100 15700000.0 0.100 15700000.0 ; OAP HAQ
[ pairs ]
; ai aj fu c0, c1, ...
1 6 1 ; OAF CAC
2 7 1 ; PAE CAB
3 6 1 ; OAG CAC
4 6 1 ; OAH CAC
5 8 1 ; OAD OAA
5 10 1 ; OAD CAI
6 9 1 ; CAC HAA
6 11 1 ; CAC OAJ
6 13 1 ; CAC CAK
7 12 1 ; CAB HAJ
7 14 1 ; CAB OAL
7 16 1 ; CAB CAM
8 11 1 ; OAA OAJ
8 13 1 ; OAA CAK
9 10 1 ; HAA CAI
10 15 1 ; CAI HAL
10 17 1 ; CAI OAN
10 19 1 ; CAI CAO
11 14 1 ; OAJ OAL
11 16 1 ; OAJ CAM
12 13 1 ; HAJ CAK
13 18 1 ; CAK HAN
13 20 1 ; CAK OAP
14 17 1 ; OAL OAN
14 19 1 ; OAL CAO
15 16 1 ; HAL CAM
16 21 1 ; CAM HAQ
17 20 1 ; OAN OAP
18 19 1 ; HAN CAO
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 2 120.0 780.0 120.0 780.0 ; OAF PAE
OAG
1 2 4 2 120.0 780.0 120.0 780.0 ; OAF PAE
OAH
1 2 5 2 109.6 450.0 109.6 450.0 ; OAF PAE
OAD
3 2 4 2 120.0 780.0 120.0 780.0 ; OAG PAE
OAH
3 2 5 2 109.6 450.0 109.6 450.0 ; OAG PAE
OAD
4 2 5 2 109.6 450.0 109.6 450.0 ; OAH PAE
OAD
2 5 6 2 120.0 530.0 120.0 530.0 ; PAE OAD
CAC
5 6 7 2 109.5 520.0 109.5 520.0 ; OAD CAC
CAB
6 7 8 2 115.0 610.0 115.0 610.0 ; CAC CAB
OAA
6 7 10 2 115.0 610.0 115.0 610.0 ; CAC CAB
CAI
8 7 10 2 115.0 610.0 115.0 610.0 ; OAA CAB
CAI
7 8 9 2 109.5 450.0 109.5 450.0 ; CAB OAA
HAA
7 10 11 2 115.0 610.0 115.0 610.0 ; CAB CAI
OAJ
7 10 13 2 115.0 610.0 115.0 610.0 ; CAB CAI
CAK
11 10 13 2 115.0 610.0 115.0 610.0 ; OAJ CAI
CAK
10 11 12 2 109.5 450.0 109.5 450.0 ; CAI OAJ
HAJ
10 13 14 2 115.0 610.0 115.0 610.0 ; CAI CAK
OAL
10 13 16 2 115.0 610.0 115.0 610.0 ; CAI CAK
CAM
14 13 16 2 115.0 610.0 115.0 610.0 ; OAL CAK
CAM
13 14 15 2 109.5 450.0 109.5 450.0 ; CAK OAL
HAL
13 16 17 2 115.0 610.0 115.0 610.0 ; CAK CAM
OAN
13 16 19 2 115.0 610.0 115.0 610.0 ; CAK CAM
CAO
17 16 19 2 115.0 610.0 115.0 610.0 ; OAN CAM
CAO
16 17 18 2 109.5 450.0 109.5 450.0 ; CAM OAN
HAN
16 19 20 2 109.5 520.0 109.5 520.0 ; CAM CAO
OAP
19 20 21 2 109.5 450.0 109.5 450.0 ; CAO OAP
HAQ
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
2 1 3 4 2 35.3 334.8 35.3 334.8 ; imp PAE OAF
OAG OAH
7 6 8 10 2 0.0 167.4 0.0 167.4 ; imp CAB CAC
OAA CAI
10 13 11 7 2 0.0 167.4 0.0 167.4 ; imp CAI CAK
OAJ CAB
13 16 14 10 2 0.0 167.4 0.0 167.4 ; imp CAK CAM
OAL CAI
16 19 17 13 2 0.0 167.4 0.0 167.4 ; imp CAM CAO
OAN CAK
6 5 2 1 1 0.0 3.1 2 0.0 3.1 2 ; dih CAC OAD
PAE OAF
7 6 5 2 1 0.0 1.3 3 0.0 1.3 3 ; dih CAB CAC
OAD PAE
5 6 7 10 1 0.0 1.0 6 0.0 1.0 6 ; dih OAD CAC
CAB CAI
6 7 8 9 1 180.0 16.7 2 180.0 16.7 2 ; dih CAC CAB
OAA HAA
13 10 7 6 1 180.0 5.9 2 180.0 5.9 2 ; dih CAK CAI
CAB CAC
7 10 11 12 1 180.0 16.7 2 180.0 16.7 2 ; dih CAB CAI
OAJ HAJ
16 13 10 7 1 180.0 5.9 2 180.0 5.9 2 ; dih CAM CAK
CAI CAB
10 13 14 15 1 180.0 16.7 2 180.0 16.7 2 ; dih CAI CAK
OAL HAL
19 16 13 10 1 180.0 5.9 2 180.0 5.9 2 ; dih CAO CAM
CAK CAI
13 16 17 18 1 180.0 16.7 2 180.0 16.7 2 ; dih CAK CAM
OAN HAN
20 19 16 13 1 0.0 1.0 6 0.0 1.0 6 ; dih OAP CAO
CAM CAK
16 19 20 21 1 0.0 1.3 3 0.0 1.3 3 ; dih CAM CAO
OAP HAQ
thanks a lot
--
*Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and
Biophysics (IBB)University of Tehran, Tehran- Iran.*
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