[gmx-users] topology file for DNA molecule

tenghl hailong at seas.ucla.edu
Fri Oct 1 17:34:01 CEST 2004


Hello Andrey,

Thanks for your suggestion. This time, that error can be avoid. However, it seems O5' can not be recognized.
Should I change the name of O5' manually? 


Fatal error: Atom O5' in residue DGUA 1 not found in rtp entry with 25 atoms
             while sorting atoms


ATOM      1  P   DGUAA   1      -8.767   1.872  20.672  1.00  0.00              
ATOM      2  O1P DGUAA   1      -9.837   2.863  20.452  1.00  0.00              
ATOM      3  O2P DGUAA   1      -8.868   0.621  19.882  1.00  0.00              
ATOM      4  O5' DGUAA   1      -7.342   2.542  20.422  1.00  0.00              
ATOM      5  C5' DGUAA   1      -6.864   3.537  21.362  1.00  0.00              
ATOM      6  C4' DGUAA   1      -6.051   4.581  20.632  1.00  0.00              


Best regards,
Hailong

*********** REPLY SEPARATOR  ***********

On 10/1/2004 at 10:50 AM Andrey V. Golovin wrote:

>hello tenghl
>about your error message it's simple =)
>just compare my conversion and yours.
>from:
>ATOM      1  P     G A   1       0.725   5.825   6.597
>ATOM      2  O1P   G A   1      -0.733   6.049   6.475
>ATOM      3  O2P   G A   1       1.328   6.176   7.902
>to:
>ATOM      1  P   DGUAA   1       0.725   5.825   6.597
>ATOM      2  O1P DGUAA   1      -0.733   6.049   6.475
>ATOM      3  O2P DGUAA   1       1.328   6.176   7.902
>
>as you can see chain ID, residue N, coordinates in the same place.
>--
>Best regards,
>Andrey                          mailto:golovin at genebee.msu.su
>
>10/1/2004, 6:16 AM you wrote:
>
>tenghl> Hello Andrey,
>
>tenghl> Thanks for your suggestion. The following is copied from my pdb
>file:
>
>tenghl> ATOM      1  P     G A   1      -8.767   1.872 
>tenghl> 20.672  1.00  0.00              
>tenghl> ATOM      2  O1P   G A   1      -9.837   2.863 
>tenghl> 20.452  1.00  0.00              
>tenghl> ATOM      3  O2P   G A   1      -8.868   0.621 
>tenghl> 19.882  1.00  0.00              
>tenghl> ATOM      4  O5'   G A   1      -7.342   2.542 
>tenghl> 20.422  1.00  0.00              
>tenghl> ATOM      5  C5'   G A   1      -6.864   3.537 
>tenghl> 21.362  1.00  0.00              
>tenghl> ATOM      6  C4'   G A   1      -6.051   4.581 
>tenghl> 20.632  1.00  0.00              
>tenghl> ATOM      7  O4'   G A   1      -4.700   4.060 
>tenghl> 20.422  1.00  0.00              
>tenghl> ATOM      8  C3'   G A   1      -6.531   4.958 
>tenghl> 19.232  1.00  0.00              
>tenghl> ATOM      9  O3'   G A   1      -6.090   6.256 
>tenghl> 18.842  1.00  0.00              
>tenghl> ATOM     10  C2'   G A   1      -5.859   3.916 
>tenghl> 18.352  1.00  0.00              
>tenghl> ............
>tenghl> ATOM    765  H3'   C B  12       8.969  -0.493 
>tenghl> 18.021  1.00  0.00              
>tenghl> ATOM    766  H6    C B  12       5.576  -2.302 
>tenghl> 17.949  1.00  0.00              
>tenghl> ATOM    767  H5    C B  12       3.536  -3.683 
>tenghl> 18.051  1.00  0.00              
>tenghl> ATOM    768  H41   C B  12       0.211  -2.100 
>tenghl> 18.439  1.00  0.00              
>tenghl> ATOM    769  H42   C B  12       1.120  -3.622  18.243  1.00  0.00
>
>
>tenghl> I followed your suggestion and the pdb file looks like
>
>tenghl> ATOM      1  P     DGUA A   1      -8.767   1.872  20.672  1.00 
>0.00
>tenghl> ATOM      2  O1P   DGUA A   1      -9.837   2.863  20.452  1.00 
>0.00
>tenghl> ATOM      3  O2P   DGUA A   1      -8.868   0.621  19.882  1.00 
>0.00
>tenghl> ATOM      4  O5'   DGUA A   1      -7.342   2.542  20.422  1.00 
>0.00
>tenghl> ATOM      5  C5'   DGUA A   1      -6.864   3.537  21.362  1.00 
>0.00
>tenghl> ATOM      6  C4'   DGUA A   1      -6.051   4.581  20.632  1.00 
>0.00
>tenghl> ATOM      7  O4'   DGUA A   1      -4.700   4.060  20.422  1.00 
>0.00
>tenghl> ATOM      8  C3'   DGUA A   1      -6.531   4.958  19.232  1.00 
>0.00
>tenghl> ATOM      9  O3'   DGUA A   1      -6.090   6.256  18.842  1.00 
>0.00
>tenghl> ATOM     10  C2'   DGUA A   1      -5.859   3.916  18.352  1.00 
>0.00
>tenghl> ......
>tenghl> ATOM    765  H3'   DCYT B  12       8.969  -0.493  18.021  1.00 
>0.00
>tenghl> ATOM    766  H6    DCYT B  12       5.576  -2.302  17.949  1.00 
>0.00
>tenghl> ATOM    767  H5    DCYT B  12       3.536  -3.683  18.051  1.00 
>0.00
>tenghl> ATOM    768  H41   DCYT B  12       0.211  -2.100  18.439  1.00 
>0.00
>tenghl> ATOM    769  H42   DCYT B  12       1.120  -3.622  18.243  1.00 
>0.00
>
>
>tenghl> However, I got the following error this time. Is
>tenghl> there anything wrong with my pdb file?
>
>tenghl> Error message:
>
>tenghl> Opening library file /space/gromacs/share/top/FF.dat
>
>tenghl> Select the Force Field:
>tenghl>  0: GROMOS96 43a1 Forcefield (official distribution)
>tenghl>  1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
>tenghl>  2: GROMOS96 43a2 Forcefield (development) (improved alkane
>dihedrals)
>tenghl>  3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>tenghl>  4: Gromacs Forcefield (see manual)
>tenghl>  5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for
>new runs)
>tenghl> 0
>tenghl> Looking whether force field file ffG43a1.rtp exists
>tenghl> Opening library file /space/gromacs/share/top/ffG43a1.rtp
>tenghl> Opening library file /space/gromacs/share/top/aminoacids.dat
>tenghl> Reading test.pdb...
>tenghl> Read 768 atoms
>tenghl> Opening library file /space/gromacs/share/top/xlateat.dat
>tenghl> 23 out of 23 lines of xlateat.dat converted succesfully
>tenghl> Analyzing pdb file
>tenghl> Fatal error: Chain identifier 'U' was used in two
>tenghl> non-sequential blocks (residue 3, atom 66)
>
>
>tenghl> Hailong
>
>tenghl> *********** REPLY SEPARATOR  ***********
>
>tenghl> On 9/30/2004 at 10:45 AM Andrey V. Golovin wrote:
>
>>>Hello tenghl,
>>>
>>>9/30/2004, 8:42 AM you wrote:
>>>
>>>first of all could you send me links for papers =) as i know gromacs
>>>was used only for trajectory analysis.
>>>And certainly you can use G43a1 ff. But first you should rename A to
>>>DADE, C to DCYT, G to DGUA, T to DTHY.
>>>
>>>tenghl> Hello Andrey,
>>>
>>>tenghl> Thank you for you reply. Is there any method that I
>>>tenghl> can use GROMACS to simulate DNA molecule?
>>>tenghl> I have read several papers which talk about the
>>>tenghl> simulation of DNA, and the software they used is GROMACS.
>>>
>>>tenghl> Thanks,
>>>
>>>tenghl> Hailong
>>>
>>>tenghl> *********** REPLY SEPARATOR  ***********
>>>
>>>tenghl> On 9/30/2004 at 10:15 AM Andrey V. Golovin wrote:
>>>
>>>>>Hello Discussion,
>>>>>
>>>>>9/30/2004, 8:15 AM you wrote:
>>>>>
>>>>>tenghl> Dear Gromacs users,?
>>>tenghl>> ?
>>>tenghl>> I am trying to build a
>>>>>topology file for a DNA model
>>>>>tenghl> using pdb2gmx -f file.pdb -p file.top -o file.gro.
>>>>>tenghl> I used OPLS force field and got the following error, any
>>>>>ideas??
>>>tenghl>> Sorting it all out...
>>>>>tenghl> Opening library file /space/gromacs/share/top/ffoplsaa.hdb
>>>>>tenghl> Opening library file
>>>>>/space/gromacs/share/top/ffoplsaa-n.tdb
>>>>>tenghl> Opening library file
>>>>>/space/gromacs/share/top/ffoplsaa-c.tdb
>>>>>tenghl> Processing chain 1 (438 atoms, 20 residues)
>>>>>tenghl> Opening library file /space/gromacs/share/top/specbond.dat
>>>>>tenghl> 5 out of 5 lines of specbond.dat converted succesfully
>>>>>tenghl> There are 0 donors and 0 acceptors
>>>>>tenghl> There are 0 hydrogen bonds
>>>>>tenghl> Fatal error: Residue 'A5' not found in residue topology
>database
>>>>>
>>>>>This happened because OPLSA ff in gromacs doesn't contain any DNA/RNA
>>>>>residues in rtp file. We added it and now busy with checking. Checking
>>>>>is necessary because we added some dihedrals. I hope soon this files
>>>>>can be found in contribution section.
>>>>>
>>>>>tenghl> ?
>>>tenghl>> Thanks
>>>>>tenghl> ?
>>>tenghl>> Hailong
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>--
>>>>>Best regards,
>>>>>Andrey                          mailto:golovin at genebee.msu.su
>>>>>
>>>>>_______________________________________________
>>>>>gmx-users mailing list
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>>>
>>>
>>>
>>>
>>>tenghl> _______________________________________________
>>>tenghl> gmx-users mailing list
>>>tenghl> gmx-users at gromacs.org
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>>>tenghl> Please don't post (un)subscribe requests to the list. Use the
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>>>
>>>
>>>
>>>--
>>>Best regards,
>>>Andrey                          mailto:golovin at genebee.msu.su
>>>
>>>_______________________________________________
>>>gmx-users mailing list
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>
>
>
>
>tenghl> _______________________________________________
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>
>
>
>--
>Best regards,
>Andrey                          mailto:golovin at genebee.msu.su
>
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