[gmx-users] topology file for DNA molecule
tenghl
hailong at seas.ucla.edu
Fri Oct 1 04:16:22 CEST 2004
Hello Andrey,
Thanks for your suggestion. The following is copied from my pdb file:
ATOM 1 P G A 1 -8.767 1.872 20.672 1.00 0.00
ATOM 2 O1P G A 1 -9.837 2.863 20.452 1.00 0.00
ATOM 3 O2P G A 1 -8.868 0.621 19.882 1.00 0.00
ATOM 4 O5' G A 1 -7.342 2.542 20.422 1.00 0.00
ATOM 5 C5' G A 1 -6.864 3.537 21.362 1.00 0.00
ATOM 6 C4' G A 1 -6.051 4.581 20.632 1.00 0.00
ATOM 7 O4' G A 1 -4.700 4.060 20.422 1.00 0.00
ATOM 8 C3' G A 1 -6.531 4.958 19.232 1.00 0.00
ATOM 9 O3' G A 1 -6.090 6.256 18.842 1.00 0.00
ATOM 10 C2' G A 1 -5.859 3.916 18.352 1.00 0.00
............
ATOM 765 H3' C B 12 8.969 -0.493 18.021 1.00 0.00
ATOM 766 H6 C B 12 5.576 -2.302 17.949 1.00 0.00
ATOM 767 H5 C B 12 3.536 -3.683 18.051 1.00 0.00
ATOM 768 H41 C B 12 0.211 -2.100 18.439 1.00 0.00
ATOM 769 H42 C B 12 1.120 -3.622 18.243 1.00 0.00
I followed your suggestion and the pdb file looks like
ATOM 1 P DGUA A 1 -8.767 1.872 20.672 1.00 0.00
ATOM 2 O1P DGUA A 1 -9.837 2.863 20.452 1.00 0.00
ATOM 3 O2P DGUA A 1 -8.868 0.621 19.882 1.00 0.00
ATOM 4 O5' DGUA A 1 -7.342 2.542 20.422 1.00 0.00
ATOM 5 C5' DGUA A 1 -6.864 3.537 21.362 1.00 0.00
ATOM 6 C4' DGUA A 1 -6.051 4.581 20.632 1.00 0.00
ATOM 7 O4' DGUA A 1 -4.700 4.060 20.422 1.00 0.00
ATOM 8 C3' DGUA A 1 -6.531 4.958 19.232 1.00 0.00
ATOM 9 O3' DGUA A 1 -6.090 6.256 18.842 1.00 0.00
ATOM 10 C2' DGUA A 1 -5.859 3.916 18.352 1.00 0.00
......
ATOM 765 H3' DCYT B 12 8.969 -0.493 18.021 1.00 0.00
ATOM 766 H6 DCYT B 12 5.576 -2.302 17.949 1.00 0.00
ATOM 767 H5 DCYT B 12 3.536 -3.683 18.051 1.00 0.00
ATOM 768 H41 DCYT B 12 0.211 -2.100 18.439 1.00 0.00
ATOM 769 H42 DCYT B 12 1.120 -3.622 18.243 1.00 0.00
However, I got the following error this time. Is there anything wrong with my pdb file?
Error message:
Opening library file /space/gromacs/share/top/FF.dat
Select the Force Field:
0: GROMOS96 43a1 Forcefield (official distribution)
1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
4: Gromacs Forcefield (see manual)
5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)
0
Looking whether force field file ffG43a1.rtp exists
Opening library file /space/gromacs/share/top/ffG43a1.rtp
Opening library file /space/gromacs/share/top/aminoacids.dat
Reading test.pdb...
Read 768 atoms
Opening library file /space/gromacs/share/top/xlateat.dat
23 out of 23 lines of xlateat.dat converted succesfully
Analyzing pdb file
Fatal error: Chain identifier 'U' was used in two non-sequential blocks (residue 3, atom 66)
Hailong
*********** REPLY SEPARATOR ***********
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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>>>www interface or send it to gmx-users-request at gromacs.org.
>
>
>
>
>tenghl> _______________________________________________
>tenghl> gmx-users mailing list
>tenghl> gmx-users at gromacs.org
>tenghl> http://www.gromacs.org/mailman/listinfo/gmx-users
>tenghl> Please don't post (un)subscribe requests to the list. Use the
>tenghl> www interface or send it to gmx-users-request at gromacs.org.
>
>
>
>--
>Best regards,
>Andrey mailto:golovin at genebee.msu.su
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
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