[gmx-users] bond between protein and DNA

[Joern Lenz]

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:

Opening library file /share/gromacs/top/aminoacids.dat
WARNING: all CONECT records are ignored

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
>>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
>>
>>
>>
>>------------------------------------------------------------------------
>>
>>_______________________________________________
>>gmx-users mailing list    gmx-users at gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please don't post (un)subscribe requests to the list. Use the 
>>www interface or send it to gmx-users-request at gromacs.org.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 


-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++