[gmx-users] problem while entering a new residue in ffgmx.rtp file
Rahul Karyappa
r.karyappa at ncl.res.in
Thu Aug 18 11:39:04 CEST 2005
Dear all,
I have a polyethylene.pdb file for 10 repeat units of
polyethylene. I want to define atoms and bonds for residue PE in the
ffgmx.rtp file. When I enter all the atoms as it is in the .pdb file
and define the bonds, I am able to run pdb2gmx. But if I
want to run pdb2gmx on higher no. of repeat units then
it will be time-consuming to define each atom and bond. Can I add atoms
and bonds for one repeat unit
and use it for any no. of length of the polymer? My .pdb file
looks like as follows:
REMARK
REMARK
REMARK This file was generated by PRODRG version 050728.0532
REMARK PRODRG written/copyrighted by Daan van Aalten
REMARK
REMARK Questions/comments to dava at davapc1.bioch.dundee.ac.uk
REMARK
REMARK When using this software in a publication, cite:
REMARK A. W. Schuettelkopf and D. M. F. van Aalten (2004).
REMARK PRODRG - a tool for high-throughput crystallography
REMARK of protein-ligand complexes.
REMARK Acta Crystallogr. D60, 1355--1363.
REMARK
REMARK
HETATM 1 CAA PE
1 1.216 1.219
-0.167 1.00
20.00
C
HETATM 2 1HAA PE
1 1.327 0.277
-0.484 1.00
20.00
H
HETATM 3 2HAA PE
1 0.787
1.218 0.736 1.00
20.00
H
HETATM 4 3HAA PE
1 0.637 1.721
-0.810 1.00
20.00
H
HETATM 5 CAB PE
1 2.587 1.894
-0.081 1.00
20.00
C
HETATM 6 1HAB PE
1 3.006 1.880
-0.989 1.00
20.00
H
HETATM 7 2HAB PE
1 3.157
1.377 0.558 1.00
20.00
H
HETATM 8 CAC PE
1 2.514
3.351 0.400 1.00
20.00
C
HETATM 9 1HAC PE
1 2.094
3.363 1.307 1.00
20.00
H
HETATM 10 2HAC PE
1 1.943 3.866
-0.239 1.00
20.00
H
HETATM 11 CAD PE
1 3.884
4.039 0.490 1.00
20.00
C
HETATM 12 1HAD PE
1 4.305 4.027
-0.417 1.00
20.00
H
HETATM 13 2HAD PE
1 4.455
3.525 1.130 1.00
20.00
H
HETATM 14 CAE PE
1 3.806
5.496 0.970 1.00
20.00
C
HETATM 15 1HAE PE
1 3.386
5.508 1.877 1.00
20.00
H
HETATM 16 2HAE PE
1 3.234
6.010 0.330 1.00
20.00
H
HETATM 17 CAF PE
1 5.176
6.185 1.059 1.00
20.00
C
HETATM 18 1HAF PE
1 5.597
6.171 0.152 1.00
20.00
H
HETATM 19 2HAF PE
1 5.747
5.672 1.700 1.00
20.00
H
HETATM 20 CAG PE
1 5.098
7.643 1.537 1.00
20.00
C
HETATM 21 1HAG PE
1 4.678
7.658 2.445 1.00
20.00
H
HETATM 22 2HAG PE
1 4.528
8.157 0.897 1.00
20.00
H
HETATM 23 CAH PE
1 6.474
8.325 1.623 1.00
20.00
C
HETATM 24 1HAH PE
1 6.871
8.339 0.705 1.00
20.00
H
HETATM 25 2HAH PE
1 7.053
7.779 2.229 1.00
20.00
H
HETATM 26 CAI PE
1 6.452
9.768 2.156 1.00
20.00
C
HETATM 27 1HAI PE
1 7.398 10.074
2.266 1.00
20.00
H
HETATM 28 2HAI PE
1 5.997
9.764 3.046 1.00
20.00
H
HETATM 29 CAJ PE
1 5.727 10.771
1.253 1.00
20.00
C
HETATM 30 1HAJ PE
1 5.759 11.679
1.670 1.00
20.00
H
HETATM 31 2HAJ PE
1 6.174 10.799
0.359 1.00
20.00
H
HETATM 32 3HAJ PE
1 4.774 10.490
1.139 1.00
20.00
H
CONECT 1 2 3 4 5
CONECT 2 1
CONECT 3 1
CONECT 4 1
CONECT 5 1 6 7 8
CONECT 6 5
CONECT 7 5
CONECT 8 5 9 10 11
CONECT 9 8
CONECT 10 8
CONECT 11 8 12 13 14
CONECT 12 11
CONECT 13 11
CONECT 14 11 15 16 17
CONECT 15 14
CONECT 16 14
CONECT 17 14 18 19 20
CONECT 18 17
CONECT 19 17
CONECT 20 17 21 22 23
CONECT 21 20
CONECT 22 20
CONECT 23 20 24 25 26
CONECT 24 23
CONECT 25 23
CONECT 26 23 27 28 29
CONECT 27 26
CONECT 28 26
CONECT 29 26 30 31 32
CONECT 30 29
CONECT 31 29
CONECT 32 29
END
-This is how I defined the residue PE in the .rtp file:
[ atoms ]
CAA C -0.2913 0
HAA1 H 0.0000 0
HAA2 H 0.1450 0
HAA3 H 0.1450 0
CAB C -0.2888 0
HAB1 H 0.1451 0
HAB2 H 0.1451 0
CAC C -0.2913 0
HAC1 H 0.1450 0
HAC2 H 0.1450 0
CAD C -0.2888 0
HAD1 H 0.1451 0
HAD2 H 0.1451 0
CAE C -0.2913 0
HAE1 H 0.1450 0
HAE2 H 0.1450 0
CAF C -0.2888 0
HAF1 H 0.1451 0
HAF2 H 0.1451 0
CAG C -0.2913 0
HAG1 H 0.1450 0
HAG2 H 0.1450 0
CAH C -0.2888 0
HAH1 H 0.1451 0
HAH2 H 0.1451 0
CAI C -0.2913 0
HAI1 H 0.1450 0
HAI2 H 0.1450 0
CAJ C -0.2888 0
HAJ1 H 0.0000 0
HAJ2 H 0.1451 0
HAJ3 H 0.1451 0
[ bonds ]
CAA 1HAA
CAA 2HAA
CAA 3HAA
CAA CAB
CAB 1HAB
CAB 2HAB
CAB CAC
CAC 1HAC
CAC 2HAC
CAC CAD
CAD 1HAD
CAD 2HAD
CAD CAE
CAE 1HAE
CAE 2HAE
CAE CAF
CAF 1HAF
CAF 2HAF
CAF CAG
CAG 1HAG
CAG 2HAG
CAG CAH
CAH 1HAH
CAH 2HAH
CAH CAI
CAI 1HAI
CAI 2HAI
CAI CAJ
CAJ 1HAJ
CAJ 2HAJ
CAJ 3HAJ
After defining them in .rtp file like this, I got the .gro and .top
file. But when I ran grompp it gave me error Fatal Error: No default
bond/angle/dihedral types, using zeroes.
Can anyone have suggestions for this?
Thank you in advance.
Rahul Karyappa
NCL, Pune
India
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