[gmx-users] transfer pdb to gro

[He, Yang]

Hi Justin,

Thank you for your reply. I have followed the regular forms about pdb file but it still shows that :

___> Opening library file /usr/share/gromacs/top/aminoacids.dat
> Opening library file /usr/share/gromacs/top/atommass.dat
> Opening library file /usr/share/gromacs/top/vdwradii.dat
> Opening library file /usr/share/gromacs/top/dgsolv.dat
> #Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
> Warning: Number of atoms in atom.pdb is 0
> WARNING: all CONECT records are ignored
> Read 0 atoms
> Volume: 0 nm^3, corresponds to roughly 0 electrons
> No velocities found
>
So I think it is because that the atom types such as Sugar ,Adenine base are not recognized  by the gromacs .Also, what I want to solve is that how to define these big atoms .

Do you know how to define these big atoms in order to make the gromacs  recognize them and creat the correct gro.file

Thank you .

Yang
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Wednesday, October 15, 2008 4:36 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] transfer pdb to gro

He, Yang wrote:
> Hi all users,
>
> When I use the editconf command to transform pdb file to gro file, it shows like this
>
> Opening library file /usr/share/gromacs/top/aminoacids.dat
> Opening library file /usr/share/gromacs/top/atommass.dat
> Opening library file /usr/share/gromacs/top/vdwradii.dat
> Opening library file /usr/share/gromacs/top/dgsolv.dat
> #Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
> Warning: Number of atoms in atom.pdb is 0
> WARNING: all CONECT records are ignored
> Read 0 atoms
> Volume: 0 nm^3, corresponds to roughly 0 electrons
> No velocities found
>
> And this is my original pdb file
>
>  ATOM   1  Ab   DNA           0.575    0.516     0.051   1.0  0.0
>  ATOM   2  Tb   DNA           0.159    2.344     0.191   1.0  0.0
>  ATOM   3  S1   DNA           2.365    6.568     1.280   1.0  0.0
>  ATOM   4  S2   DNA           2.365   -6.568    -1.280   1.0  0.0
>  ATOM   5  P1   DNA           -0.628   8.896     2.186   1.0  0.0
>  ATOM   6  P2   DNA           -0.628  -8.896    -2.186   1.0  0.0
>  ATOM   7  S3   DNA          -1.947    6.704    -4.660   1.0  0.0
>  ATOM   8  S4   DNA          -1.947   -6.704     4.660   1.0  0.0
> CONECT  1  3
> CONECT  2  4
> CONECT  3  1  5
> CONECT  4  2  6
> CONECT  5  3  7
> CONECT  6  4  8
> CONECT  7  5
> CONECT  8  6
> MASTER        0    0    0    0    0    0    0    0   8    0   8    0
> END
>
> not very complex, only 8 atoms .  And I find these atoms are not included in the gromacs so i defined them in the .atp file this
>
>  Ab  134.1;   Adenine base of DNA
>  Tb  125.1;   Thymine base of DNA
>  S   83.11;   Sugar of DNA
>  P   94.97;   Phosphate of DNA
>
>

The .atp file means nothing for editconf.

>  Can anyone of you help me sovle this problem?
>

It looks like the formatting of your .pdb file is irregular.  A fixed format is
required for proper detection of atoms and coordinates.  See here:

http://www.wwpdb.org/docs.html

-Justin

> Thank you in advance
>
> Yang He
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--
========================================

Justin A. Lemkul
Graduate Research Assistant
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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