Dear Daniel,
>To use these parameters I added the following lines to my leaprc
>frcmod_nad+ = loadamberparams frcmod.NAD+
>loadOff NAD+.lib
You don't need the frcmod_nad+ unit you can just do loadamberparams
frcmod.NAD+ this will overwrite the currently defined parameters (which are
none since the NAD+ is built with it's own unique atom types). Thus loading
the frcmod file will just add new parameters.
Avoid the use of + in unit names, this probably isn't a problem but it is
good practice to use "standard" characters where possible.
>If I open the structure with "edit a" I get the editor with
I'm not sure what you did here. The unit name for the NAD+ unit is NDP and
for the NADH unit is NAD... See amber8/dat/contrib/NADH_and_NAD+/0README for
more info.
>Sourcing leaprc: ./leaprc
>Log file: ./leap.log
>Loading Prep file: ./nad+.prep
This is strange. There is no nad+.prep file in my parameter set. Where did
you find this???
Do the following...
Download
http://pharmacy.man.ac.uk/amber/cof/NAD+.lib
http://pharmacy.man.ac.uk/amber/cof/frcmod.NAD+
See
http://pharmacy.man.ac.uk/amber/cof/NAD_inf.html for info and
references.
Edit your PDB file and replace the NAD+ unit's residue name with NDP.
Then load leap:
$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
Now load in the off file and frcmod files:
>loadamberparams frcmod.NAD+
>loadoff NAD+.lib
Look at the NDP unit if you want.
>edit NDP
Then you can load your pdb file as a new unit and assuming you renamed all
the NAD+ residues as NDP it should load fine.
All the best
Ross
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|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
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Received on Tue Jul 05 2005 - 16:53:01 PDT
