[gmx-users] transfer pdb to gro

[Justin A. Lemkul]

He, Yang wrote:
> 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
>>

Then you haven't followed the format correctly.

I created the following from your 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

It successfully creates a .gro file.

-Justin

> 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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-- 
========================================

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

========================================