[gmx-users] bond between protein and DNA

[Joern Lenz]

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
yours
joe 

-------------- next part --------------
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
yours
joe