Joern Lenz wrote:
On Wednesday 16 August 2006 16:32, you wrote:
dear gromacs users,
i am new to gromacs (using version 3.3.1) and trying to simulate an enzyme
which is covalently bound to a piece of dna i.e. a tyrosine is connected to
the dna backbone establishing a phosphodiester group.
but each time i try to start the simulation using the G43a1 forcefield
there occurs a warning like
WARNING 1 [file "blah.itp", line 1020]:
No default G96Angle types, using zeroes
or
WARNING 39 [file "blah.itp", line 1509]:
No default Proper Dih. types, using zeroes
i browsed to the mailing list archive and found lots of problems similar to
mine but - forgive me - i am not able to fix my problem with these hints.
i know that i have to add these angles and dihedrals in the itp or rtp
files. But where exactly and how.
one example oif a missing angle is the connection from one nucleeotide to
the next in the DNA (O3* - P - O1P).
Can anyone tell me how to add the missing lines and where to do that
exactly (perhaps with a little example) ???
That would be of great help for me. Otherwise I will die unhappy ...
Another problem is: where to tell GROMACS that there is a connective bond,
angle, dihedral between an aminoacid (the phenolic group of tyrosine) and
the DNA backbone ?
So if you have any suggestions that could help me, be so kind and try to
answer my question.
Have a nice day
Joe
_______________________________________________
gmx-users mailing list [email protected]
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
first you probably need to use another force field like amber or opls
since gromos is not very well suited for DNA.
you can define a special bond in the specbond.dat file. copy it to your
working dir and edit it as appropriate.
--
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list [email protected]
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
