On 8/18/13 1:23 AM, Musharaf Ali wrote:
Dear Justin
Again thanks. Actually the problem arises in the running of pdb2gmx of pdb
file of crown ether. I have generated the pdb file from xyz coordinates
using openbabel. The pdb file looks like below.
COMPND D:\data-structure\18c6.xyz
AUTHOR GENERATED BY OPEN BABEL 2.3.2
HETATM 1 O LIG 1 0.000 0.000 0.000 1.00 0.00 O
HETATM 2 C LIG 1 0.000 0.000 1.400 1.00 0.00 C
HETATM 3 C LIG 1 1.367 0.000 1.883 1.00 0.00 C
HETATM 4 H LIG 1 -0.513 0.889 1.763 1.00 0.00 H
HETATM 5 H LIG 1 -0.513 -0.889 1.763 1.00 0.00 H
HETATM 6 H LIG 1 1.367 0.000 2.972 1.00 0.00 H
HETATM 7 O LIG 1 2.027 -1.143 1.417 1.00 0.00 O
HETATM 8 H LIG 1 1.880 0.889 1.520 1.00 0.00 H
HETATM 9 C LIG 1 3.347 -1.143 1.883 1.00 0.00 C
HETATM 10 C LIG 1 4.031 -2.327 1.400 1.00 0.00 C
HETATM 11 H LIG 1 3.860 -0.254 1.520 1.00 0.00 H
HETATM 12 H LIG 1 3.347 -1.143 2.972 1.00 0.00 H
HETATM 13 H LIG 1 5.057 -2.327 1.763 1.00 0.00 H
HETATM 14 H LIG 1 3.517 -3.216 1.763 1.00 0.00 H
HETATM 15 O LIG 1 4.031 -2.327 -0.000 1.00 0.00 O
HETATM 16 C LIG 1 4.690 -3.470 -0.467 1.00 0.00 C
HETATM 17 C LIG 1 4.690 -3.470 -1.917 1.00 0.00 C
HETATM 18 H LIG 1 5.717 -3.470 -0.104 1.00 0.00 H
HETATM 19 H LIG 1 4.177 -4.359 -0.104 1.00 0.00 H
HETATM 20 H LIG 1 5.204 -4.359 -2.280 1.00 0.00 H
HETATM 21 O LIG 1 3.371 -3.470 -2.383 1.00 0.00 O
HETATM 22 H LIG 1 5.204 -2.581 -2.280 1.00 0.00 H
HETATM 23 C LIG 1 3.371 -3.470 -3.783 1.00 0.00 C
HETATM 24 C LIG 1 2.003 -3.470 -4.267 1.00 0.00 C
HETATM 25 H LIG 1 3.884 -2.581 -4.146 1.00 0.00 H
HETATM 26 H LIG 1 3.884 -4.359 -4.146 1.00 0.00 H
HETATM 27 H LIG 1 2.003 -3.470 -5.356 1.00 0.00 H
HETATM 28 H LIG 1 1.490 -4.359 -3.904 1.00 0.00 H
HETATM 29 O LIG 1 1.343 -2.327 -3.800 1.00 0.00 O
HETATM 30 C LIG 1 0.024 -2.327 -4.267 1.00 0.00 C
HETATM 31 C LIG 1 -0.660 -1.143 -3.783 1.00 0.00 C
HETATM 32 H LIG 1 0.024 -2.327 -5.356 1.00 0.00 H
HETATM 33 H LIG 1 -0.490 -3.216 -3.904 1.00 0.00 H
HETATM 34 H LIG 1 -1.687 -1.143 -4.146 1.00 0.00 H
HETATM 35 O LIG 1 -0.660 -1.143 -2.383 1.00 0.00 O
HETATM 36 H LIG 1 -0.147 -0.254 -4.146 1.00 0.00 H
HETATM 37 C LIG 1 -1.320 0.000 -1.917 1.00 0.00 C
HETATM 38 C LIG 1 -1.320 0.000 -0.467 1.00 0.00 C
HETATM 39 H LIG 1 -0.807 0.889 -2.280 1.00 0.00 H
HETATM 40 H LIG 1 -2.347 0.000 -2.280 1.00 0.00 H
HETATM 41 H LIG 1 -1.833 0.889 -0.104 1.00 0.00 H
HETATM 42 H LIG 1 -1.833 -0.889 -0.104 1.00 0.00 H
CONECT 1 38 2
CONECT 2 1 5 4 3
CONECT 2
CONECT 3 2 7 8 6
CONECT 3
CONECT 4 2
CONECT 5 2
CONECT 6 3
CONECT 7 9 3
CONECT 8 3
CONECT 9 10 7 11 12
CONECT 9
CONECT 10 15 13 14 9
CONECT 10
CONECT 11 9
CONECT 12 9
CONECT 13 10
CONECT 14 10
CONECT 15 16 10
CONECT 16 17 18 19 15
CONECT 16
CONECT 17 21 22 20 16
CONECT 17
CONECT 18 16
CONECT 19 16
CONECT 20 17
CONECT 21 23 17
CONECT 22 17
CONECT 23 24 26 25 21
CONECT 23
CONECT 24 27 28 29 23
CONECT 24
CONECT 25 23
CONECT 26 23
CONECT 27 24
CONECT 28 24
CONECT 29 24 30
CONECT 30 32 33 29 31
CONECT 30
CONECT 31 30 36 34 35
CONECT 31
CONECT 32 30
CONECT 33 30
CONECT 34 31
CONECT 35 31 37
CONECT 36 31
CONECT 37 35 39 40 38
CONECT 37
CONECT 38 37 41 42 1
CONECT 38
CONECT 39 37
CONECT 40 37
CONECT 41 38
CONECT 42 38
MASTER 0 0 0 0 0 0 0 0 42 0 42 0
END
Now my query is whether this pdb format i can directly used for pdb2gmx or
i have to change the "LIG" temr to OPLS force field term. If you can guide
here then the problem will be sorted out.
I would suggest you spend a while with some tutorial material and the manual to
understand the inner mechanics of a normal workflow, then move on to custom
residues. Proper implementation is not easy and getting pdb2gmx to deal with a
cyclic molecule is not trivial. You will need to define suitable entries in the
.rtp file and specbond.dat. Consult the list archive for tips - discussions on
cyclic peptides and polymers will have relevant information.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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