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
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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