[gmx-users] Re: DNA and GROMACS/GROMOS87

[Graham Smith]

Hi - 

Further to previous comments, most X-ray DNA structures will, of 
course, lack H so if you want the Hs that are in the ffgmx residues
to be added, you need to put 

DAD     1
        2       3       N6      C6      N1
DCY     1 
        2       3       N4      C4      N3
DGU     2
        1       1       N1      C2      C6  
        2       3       N2      C2      N1
DTH     1 
        1       1       N3      C2      C4 

into ffgmx.hdb. Even with this, pdb2gmx (post version 3.0)  still
needs the -missing flag, or it will choke on the 5' end, which lacks a
phosphate. (This is another way of saying the termini aren't done).

BTW I think the order of spaces in sed is sed 's/  A /DADE/' etc

As Anton and John say, though, this looks like a pretty poor 
forcefield. I only used it for someone who'd built a DNA-protein 
model with bad contacts and just wanted to minimize them away. 
I bet it won't work with full MD. 

The last news on this (6th Nov) was that Amber had been ported
to gromacs by Eric Sorin in Pande's group and tests were under way. 
When they are finished, it's going to be put in the CVS tree. 
I'd be tempted to wait for this. 

-Graham

########################################################################

Dr. Graham R. Smith,
Biomolecular Modelling Laboratory,
Cancer Research UK,
44 Lincoln's Inn Fields,
London WC2A 3PX,
U.K.
Tel: +44-(0)20 7269 3348
email: graham.smith at cancer.org.uk
URL: http://www.bmm.icnet.uk/~smithgr