[gmx-users] topology file for DNA molecule
Andrey V. Golovin
golovin at genebee.msu.su
Fri Oct 1 08:50:58 CEST 2004
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> _______________________________________________
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>>
>>
>>
>>--
>>Best regards,
>>Andrey mailto:golovin at genebee.msu.su
>>
>>_______________________________________________
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tenghl> _______________________________________________
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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
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