[gmx-users] bond between protein and DNA

[David van der Spoel]

Joern Lenz wrote:
> 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 ?

Are you sure? You have to generate correct starting structure in that case.
pdb2gmx connects the DNA to protein if the distance is within 10 % of 
what you specify in the specbond.dat file.
> 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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