[gmx-users] generation of gro file

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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