[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
>>>>>gmx-users at gromacs.org
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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
>>>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
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>>>http://www.gromacs.org/mailman/listinfo/gmx-users
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>
>
>
>
>tenghl> _______________________________________________
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>
>
>
>--
>Best regards,
>Andrey mailto:golovin at genebee.msu.su
>
>_______________________________________________
>gmx-users mailing list
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