here is all information. I attached 2 attachment to my privious mail. It
looks 2nd didn't come. Sorry. Here I am giving details.
I am using opls force field . I added "PCD" as residue name in
aminoacid.dat file.
pdb2gmx -f dioxin.pdb -o di.pdb -p di.top -ter
i have attached input:dioxin.pdb, output:di.pdb and di.top
here I have pasted the parameters from .rtp file.
[ PCD ]
[ atoms ]
O opls_186 -0.3088 1
C2 opls_263 0.2336 2
C3 opls_263 0.2336 2
O4 opls_186 -0.3088 1
C5 opls_263 0.2336 2
C6 opls_263 0.2336 2
C7 opls_263 -0.2325 2
C8 opls_263 0.0907 2
C9 opls_263 0.0908 2
C10 opls_263 -0.2326 2
C11 opls_263 -0.2326 2
C12 opls_263 0.0907 2
C13 opls_263 0.0907 2
C14 opls_263 -0.2325 2
CL1 opls_264 -0.0986 3
CL2 opls_264 -0.0986 3
CL3 opls_264 -0.0986 3
CL4 opls_264 -0.0986 3
H19 opls_146 0.1612 4
H20 opls_146 0.1612 4
H21 opls_146 0.1612 4
H22 opls_146 0.1612 4
[ bonds ]
O C2
C2 C3
C3 O4
O4 C5
C5 C6
C6 O
C3 C7
C7 C8
C8 C9
C9 C10
C10 C2
C5 C11
C11 C12
C12 C13
C13 C14
C14 C6
C8 CL1
C9 CL2
C12 CL4
C13 CL4
C10 H19
C7 H20
C14 H21
C11 H22
REMARK Accelrys Discovery Studio PDB file
REMARK Created: Sat Nov 14 17:45:28 Eastern Standard Time 2009
ATOM 1 O1 PCD 1 0.000 -1.428 0.001 1.00 0.00 O
ATOM 2 C2 PCD 1 1.172 -0.699 0.001 1.00 0.00 C
ATOM 3 C3 PCD 1 1.172 0.700 0.001 1.00 0.00 C
ATOM 4 O4 PCD 1 0.000 1.428 0.001 1.00 0.00 O
ATOM 5 C5 PCD 1 -1.172 0.700 0.001 1.00 0.00 C
ATOM 6 C6 PCD 1 -1.172 -0.700 0.001 1.00 0.00 C
ATOM 7 C7 PCD 1 2.372 1.395 0.000 1.00 0.00 C
ATOM 8 C8 PCD 1 3.586 0.700 -0.000 1.00 0.00 C
ATOM 9 C9 PCD 1 3.586 -0.700 -0.000 1.00 0.00 C
ATOM 10 C10 PCD 1 2.372 -1.395 0.000 1.00 0.00 C
ATOM 11 C11 PCD 1 -2.372 1.395 0.000 1.00 0.00 C
ATOM 12 C12 PCD 1 -3.586 0.700 -0.000 1.00 0.00 C
ATOM 13 C13 PCD 1 -3.586 -0.700 -0.000 1.00 0.00 C
ATOM 14 C14 PCD 1 -2.372 -1.395 0.000 1.00 0.00 C
ATOM 15 CL1 PCD 1 5.070 1.618 -0.001 1.00 0.00 CL
ATOM 16 CL2 PCD 1 5.070 -1.618 -0.001 1.00 0.00 CL
ATOM 17 CL3 PCD 1 -5.070 1.618 -0.001 1.00 0.00 CL
ATOM 18 CL4 PCD 1 -5.070 -1.618 -0.001 1.00 0.00 CL
ATOM 19 H19 PCD 1 2.359 -2.478 0.000 1.00 0.00 H
ATOM 20 H20 PCD 1 2.359 2.478 0.000 1.00 0.00 H
ATOM 21 H21 PCD 1 -2.359 -2.478 0.000 1.00 0.00 H
ATOM 22 H22 PCD 1 -2.359 2.478 0.000 1.00 0.00 H
END
TITLE Giant Rising Ordinary Mutants for A Clerical Setup
MODEL 1
ATOM 1 O PCD 1 0.000 -1.428 0.001 1.00 0.00
ATOM 2 C2 PCD 1 1.172 -0.699 0.001 1.00 0.00
ATOM 3 C3 PCD 1 1.172 0.700 0.001 1.00 0.00
ATOM 4 O4 PCD 1 0.000 1.428 0.001 1.00 0.00
ATOM 5 C5 PCD 1 -1.172 0.700 0.001 1.00 0.00
ATOM 6 C6 PCD 1 -1.172 -0.700 0.001 1.00 0.00
ATOM 7 C7 PCD 1 2.372 1.395 0.000 1.00 0.00
ATOM 8 C8 PCD 1 3.586 0.700 -0.000 1.00 0.00
ATOM 9 C9 PCD 1 3.586 -0.700 -0.000 1.00 0.00
ATOM 10 C10 PCD 1 2.372 -1.395 0.000 1.00 0.00
ATOM 11 C11 PCD 1 -2.372 1.395 0.000 1.00 0.00
ATOM 12 C12 PCD 1 -3.586 0.700 -0.000 1.00 0.00
ATOM 13 C13 PCD 1 -3.586 -0.700 -0.000 1.00 0.00
ATOM 14 C14 PCD 1 -2.372 -1.395 0.000 1.00 0.00
ATOM 15 CL1 PCD 1 5.070 1.618 -0.001 1.00 0.00
ATOM 16 CL2 PCD 1 5.070 -1.618 -0.001 1.00 0.00
ATOM 17 CL3 PCD 1 -5.070 1.618 -0.001 1.00 0.00
ATOM 18 CL4 PCD 1 -5.070 -1.618 -0.001 1.00 0.00
ATOM 19 H19 PCD 1 2.359 -2.478 0.000 1.00 0.00
ATOM 20 H20 PCD 1 2.359 2.478 0.000 1.00 0.00
ATOM 21 H21 PCD 1 -2.359 -2.478 0.000 1.00 0.00
ATOM 22 H22 PCD 1 -2.359 2.478 0.000 1.00 0.00
TER
ENDMDL
;
; File 'di.top' was generated
; By user: ndhumal (36026)
; On host: c22
; At date: Tue Nov 17 08:27:33 2009
;
; This is your topology file
; "Move about like a Scientist, lay down, get kissed" (Red Hot Chili
Peppars)
;
; Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
1 opls_186 1 PCD O 1 -0.3088 15.9994 ; qtot
-0.3088
2 opls_263 1 PCD C2 2 0.2336 12.011 ; qtot
-0.0752
3 opls_263 1 PCD C3 2 0.2336 12.011 ; qtot
0.1584
4 opls_186 1 PCD O4 3 -0.3088 15.9994 ; qtot
-0.1504
5 opls_263 1 PCD C5 4 0.2336 12.011 ; qtot
0.0832
6 opls_263 1 PCD C6 4 0.2336 12.011 ; qtot
0.3168
7 opls_263 1 PCD C7 4 -0.2325 12.011 ; qtot
0.0843
8 opls_263 1 PCD C8 4 0.0907 12.011 ; qtot
0.175
9 opls_263 1 PCD C9 4 0.0908 12.011 ; qtot
0.2658
10 opls_263 1 PCD C10 4 -0.2326 12.011 ; qtot
0.0332
11 opls_263 1 PCD C11 4 -0.2326 12.011 ; qtot
-0.1994
12 opls_263 1 PCD C12 4 0.0907 12.011 ; qtot
-0.1087
13 opls_263 1 PCD C13 4 0.0907 12.011 ; qtot
-0.018
14 opls_263 1 PCD C14 4 -0.2325 12.011 ; qtot
-0.2505
15 opls_264 1 PCD CL1 5 -0.0986 35.453 ; qtot
-0.3491
16 opls_264 1 PCD CL2 5 -0.0986 35.453 ; qtot
-0.4477
17 opls_264 1 PCD CL3 5 -0.0986 35.453 ; qtot
-0.5463
18 opls_264 1 PCD CL4 5 -0.0986 35.453 ; qtot
-0.6449
19 opls_146 1 PCD H19 6 0.1612 1.008 ; qtot
-0.4837
20 opls_146 1 PCD H20 6 0.1612 1.008 ; qtot
-0.3225
21 opls_146 1 PCD H21 6 0.1612 1.008 ; qtot
-0.1613
22 opls_146 1 PCD H22 6 0.1612 1.008 ; qtot
-0.0001
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 6 1
2 3 1
2 10 1
3 4 1
3 7 1
4 5 1
5 6 1
5 11 1
6 14 1
7 8 1
7 20 1
8 9 1
8 15 1
9 10 1
9 16 1
10 19 1
11 12 1
11 22 1
12 13 1
12 18 1
13 14 1
13 18 1
14 21 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 4 1
1 7 1
1 9 1
1 11 1
1 13 1
1 19 1
1 21 1
2 5 1
2 8 1
2 14 1
2 16 1
2 20 1
3 6 1
3 9 1
3 11 1
3 15 1
3 19 1
4 8 1
4 10 1
4 12 1
4 14 1
4 20 1
4 22 1
5 7 1
5 13 1
5 18 1
5 21 1
6 10 1
6 12 1
6 18 1
6 22 1
7 10 1
7 16 1
8 19 1
9 20 1
10 15 1
11 14 1
12 21 1
13 22 1
15 16 1
15 20 1
16 19 1
18 21 1
18 22 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 6 1
1 2 3 1
1 2 10 1
3 2 10 1
2 3 4 1
2 3 7 1
4 3 7 1
3 4 5 1
4 5 6 1
4 5 11 1
6 5 11 1
1 6 5 1
1 6 14 1
5 6 14 1
3 7 8 1
3 7 20 1
8 7 20 1
7 8 9 1
7 8 15 1
9 8 15 1
8 9 10 1
8 9 16 1
10 9 16 1
2 10 9 1
2 10 19 1
9 10 19 1
5 11 12 1
5 11 22 1
12 11 22 1
11 12 13 1
11 12 18 1
13 12 18 1
12 13 14 1
12 13 18 1
14 13 18 1
6 14 13 1
6 14 21 1
13 14 21 1
12 18 13 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
c3 c4 c5
6 1 2 3 3
6 1 2 10 3
2 1 6 5 3
2 1 6 14 3
1 2 3 4 3
1 2 3 7 3
10 2 3 4 3
10 2 3 7 3
1 2 10 9 3
1 2 10 19 3
3 2 10 9 3
3 2 10 19 3
2 3 4 5 3
7 3 4 5 3
2 3 7 8 3
2 3 7 20 3
4 3 7 8 3
4 3 7 20 3
3 4 5 6 3
3 4 5 11 3
4 5 6 1 3
4 5 6 14 3
11 5 6 1 3
11 5 6 14 3
4 5 11 12 3
4 5 11 22 3
6 5 11 12 3
6 5 11 22 3
1 6 14 13 3
1 6 14 21 3
5 6 14 13 3
5 6 14 21 3
3 7 8 9 3
3 7 8 15 3
20 7 8 9 3
20 7 8 15 3
7 8 9 10 3
7 8 9 16 3
15 8 9 10 3
15 8 9 16 3
8 9 10 2 3
8 9 10 19 3
16 9 10 2 3
16 9 10 19 3
5 11 12 13 3
5 11 12 18 3
22 11 12 13 3
22 11 12 18 3
11 12 13 14 3
11 12 13 18 3
18 12 13 14 3
11 12 18 13 3
12 13 14 6 3
12 13 14 21 3
18 13 14 6 3
18 13 14 21 3
14 13 18 12 3
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
Protein 1--
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