AMBER Archive (2005)

Subject: Re: AMBER: How to deal with the Non-standard residue

From: FyD (fyd_at_u-picardie.fr)
Date: Mon Apr 25 2005 - 15:07:33 CDT

> Now I have a protein which contains one non-standard residue "CME".
> But there is no parameter in AMBER7 or AMBER8. Although the CME atoms
> are indicated as hetero atoms by "HETATM", the residue CME connect with
> other standard residues. For example:
>
> ATOM 251 O THR A 193 -4.451 13.561 10.631 O
> ATOM 252 CB THR A 193 -3.183 16.320 9.115 C
> ATOM 253 OG1 THR A 193 -1.928 16.821 8.633 O
> ATOM 254 CG2 THR A 193 -3.307 16.825 10.598 C
> HETATM 255 N CME A 194 -5.628 14.444 9.024 N
> HETATM 256 CA CME A 194 -6.937 13.873 9.179 C
> HETATM 257 CB CME A 194 -8.004 14.140 8.141 C
> HETATM 258 SG CME A 194 -9.536 13.697 8.934 S
> HETATM 259 SD CME A 194 -9.892 14.927 10.558 S
> HETATM 260 CE CME A 194 -10.809 14.171 11.870 C
> HETATM 261 CZ CME A 194 -10.005 13.101 12.561 C
> HETATM 262 OH CME A 194 -10.545 12.502 13.488 O
> HETATM 263 C CME A 194 -6.856 12.436 9.638 C
> HETATM 264 O CME A 194 -6.870 12.150 10.820 O
> ATOM 265 N ILE A 195 -6.433 11.576 8.699 N
> ATOM 266 CA ILE A 195 -6.311 10.129 8.990 C
> ATOM 267 C ILE A 195 -5.295 9.629 10.047 C
> ATOM 268 O ILE A 195 -5.576 8.680 10.762 O
>
> How do I add the parameters of CME?

You could use R.E.D. to generate a tripos file that you could load in LEaP to
generate an OFF file. See:
http://www.u-picardie.fr/labo/lbpd/RED/
 &
http://www.u-picardie.fr/labo/lbpd/RED/FAQ-I.htm

Regards, Francois

  F.-Y. Dupradeau
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
The Scripps Research Institute, La Jolla, CA, USA
       --
http://www.u-picardie.fr/labo/lbpd/FyD.htm
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu