[gmx-users] bond between protein and DNA

David van der Spoel spoel at xray.bmc.uu.se
Fri Aug 25 11:32:26 CEST 2006

Joern Lenz wrote:
> First of all: Many thanks to you, David. Without your help i would not have 
> got so far.
> I think my input structure is fine and using chimera e.g. for viewing,  the 
> connection bewteen the Tyr-OH and the P of the DNA backbone is fine. But 
> using pdb2gmx produces the following warning:

pdb2gmx print a distance matrix for the special bonds and it tells you 
what is connected to what.

> Opening library file /share/gromacs/top/aminoacids.dat
> WARNING: all CONECT records are ignored
CONECT records are unreliable and therefore gromacs ignores them.

> Can that warning be connected with my problem that the wrong dna strand is 
> connected to the protein? In an earlier you wrote that if if i only use dna 
> everything is fine but else not. Obvious i use DNA and it seems not to be 
> fine. how can i fix this warning ? what do i have to modify and where ? 
> Many thanks. I guess I owe you a beer.
> Greetings
> Joern
> 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
>>> 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 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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