[gmx-users] bond between protein and DNA

[Joern Lenz]

Thanks so far.
the protein and the one dna strand are now regarded to be one molecule, but it 
is the wrong strand of the dna and i do not know who to tell pdb2gmx to use 
not this but the other dna strand which has a 4 bases overlap with which is 
is bound to the tyrosine OH
is there anybody who has a suggestion that may help me fix this ?
thank you so much
joe


Joern Lenz wrote:
> dear guys,
> sorry to ask again, but i still have a problem with my simulation and i am 
very new to gromacs.
> my system consists of a protein and a DNA which are covalently connected, 
i.e.
> there is a connecting bond between the P of the DNA backbone and an OH of a 
tyrosine.
> what i have done so far is (thanks prof. van der spoel): i added a line to 
the specbond.dat file so that this file now looks like:
> 6
> CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
> CYS SG 1 HEME FE 2 0.25 CYS2 HEME
> CYS SG 1 HEME CAB 1 0.2 CYS2 HEME
> CYS SG 1 HEME CAC 1 0.2 CYS2 HEME
> HIS NE2 1 HEME FE 1 0.2 HIS1 HEME
> TYR OH 1 DGUA P 1 0.16 TYR DGUA
> my top file looks like:
> #include "ffoplsaa.itp"
> #include "blah_A.itp"
> #include "blah_B.itp"
> #include "spc.itp"
> ...
> where blah_A.itp is the protein and blah_2.itp is the DNA, so i cannot 
verify if two atoms, one of DNA and one of protein are connected as i want 
them to be 'cause they occur in differnt itp files.
> in the mailing list i read that i have to add something to the rtp file, 
too. but what and how (i mean the dna and the protein are in differnt itp 
files)
> so many many thanks for helping in advance

you need to rerun pdb2gmx with the specbond.dat file preset. It will now 
generate the bond and treat your complex as a single molecule and 
generate a topology for that molecule.

> yours
> joe
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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