[gmx-users] transfer pdb to gro

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 16 02:48:11 CEST 2008 


He, Yang wrote:
>  So you have created the gro.file . I have tried your pdb.file again but it still can not create the gro.file. It is really strange. Can you show me the gro.file created based on the pdb.file?
> 

The .gro I created was:

Gyas ROwers Mature At Cryogenic Speed
     8
     1DNA     Ab    1   0.058   0.052   0.000
     1DNA     Tb    2   0.016   0.234   0.010
     1DNA     S1    3   0.236   0.657   0.120
     1DNA     S2    4   0.236  -0.657  -0.120
     1DNA     P1    5  -0.063   0.890   0.210
     1DNA     P2    6  -0.063  -0.890  -0.210
     1DNA     S3    7  -0.195   0.670  -0.460
     1DNA     S4    8  -0.195  -0.670   0.460
    0.00000   0.00000   0.00000

When running editconf (using the .pdb I pasted below), it correctly detects 8 atoms.

-Justin

> Thank you.
> 
> Yang He
> ________________________________________
> From: Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Wednesday, October 15, 2008 5:27 PM
> To: He, Yang; Gromacs Users' List
> Subject: Re: [gmx-users] transfer pdb to gro
> 
> 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
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
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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
> 
> ========================================
> 

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

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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