AMBER Archive (2005)

Subject: RE: AMBER: Problems with parameter lib and prep püarameter files

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jul 05 2005 - 10:47:22 CDT

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_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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