[gmx-users] The .pdb file compatible with structure of .itp file,

[Justin Lemkul]

On 9/6/12 3:51 PM, Ali Alizadeh wrote:
> Dear Justin
>
> Thank you for your reply.
> But i knew that,
> i have a .itp file for example: heptane.itp:
>
> [ moleculetype ]
> ; Name	nrexcl
> HEP	3
>
> [ atoms ]
> ; nr    type   	resnr  	residu  atom  	cgnr	charge
> 1	CH3	1       LIG	CH31	1	0.0
> 2	CH2	1	LIG	CH22	2	0.0
> 3	CH2	1	LIG	CH23	3	0.0
> 4	CH2	1	LIG	CH24	4	0.0
> 5	CH2	1	LIG	CH25	5	0.0
> 6	CH2	1	LIG	CH26	6	0.0
> 7       CH3     1       LIG     CH37    7       0.0
> [ bonds ]
> ; i	j
> 1	2
> 2	3
> 3	4
> 4	5
> 5	6
> 6       7
>
> [ angles ]
> ; i	j	k
> 1	2	3
> 2	3	4
> 3	4	5
> 4	5	6
> 5       6       7
>
> [ dihedrals ]
> ; i	j	k 	l	type
> 1 	2	3	4	3
> 2	3	4	5	3
> 3	4	5	6	3
> 4       5       6       7       3
>
> and my pdb file for heptane:
>
> COMPND    UNNAMED
> AUTHOR    GENERATED BY OPEN BABEL 2.3.0
> ATOM      1  C   LIG     1      -5.231   0.634  -0.427  1.00  0.00           C
> ATOM      2  H   LIG     1      -5.407  -0.100  -1.242  1.00  0.00           H
> ATOM      3  H   LIG     1      -5.768   1.574  -0.673  1.00  0.00           H
> ATOM      4  H   LIG     1      -5.641   0.230   0.523  1.00  0.00           H
> ATOM      5  C   LIG     1      -3.739   0.920  -0.284  1.00  0.00           C
> ATOM      6  H   LIG     1      -3.595   1.672   0.522  1.00  0.00           H
> ATOM      7  H   LIG     1      -3.377   1.346  -1.242  1.00  0.00           H
> ATOM      8  C   LIG     1      -2.963  -0.360   0.064  1.00  0.00           C
> ATOM      9  H   LIG     1      -3.379  -0.775   1.009  1.00  0.00           H
> ATOM     10  H   LIG     1      -3.101  -1.119  -0.737  1.00  0.00           H
> ATOM     11  C   LIG     1      -0.728   0.352  -0.983  1.00  0.00           C
> ATOM     12  H   LIG     1      -0.896  -0.406  -1.780  1.00  0.00           H
> ATOM     13  H   LIG     1      -1.130   1.324  -1.336  1.00  0.00           H
> ATOM     14  C   LIG     1       0.790   0.492  -0.786  1.00  0.00           C
> ATOM     15  H   LIG     1       1.220  -0.478  -0.454  1.00  0.00           H
> ATOM     16  H   LIG     1       1.242   0.752  -1.768  1.00  0.00           H
> ATOM     17  C   LIG     1      -1.461  -0.115   0.288  1.00  0.00           C
> ATOM     18  H   LIG     1      -1.340   0.624   1.106  1.00  0.00           H
> ATOM     19  H   LIG     1      -1.009  -1.077   0.616  1.00  0.00           H
> ATOM     20  C   LIG     1       1.172   1.589   0.209  1.00  0.00           C
> ATOM     21  H   LIG     1       0.797   1.360   1.226  1.00  0.00           H
> ATOM     22  H   LIG     1       0.764   2.568  -0.123  1.00  0.00           H
> ATOM     23  H   LIG     1       2.278   1.667   0.264  1.00  0.00           H
>
> Above file is only for one molecule.
>
> How to i use this pdb file for the .itp file ?(If i have 1000 heptane molecules)
> Can I use VMD software?
>

I don't know if VMD can do that.  You can easily remove the H atoms with a 
simple grep command (grep -v H heptane.pdb > heptane_noH.pdb).  Then you need to 
rename the atoms as the topology expects.  Building a box of 1000 heptane 
molecules can be done with Gromacs tools using this "clean" coordinate file. 
See http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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