AMBER Archive (2000)

Subject: (no subject)

From: jramon_at_husky.bq.ub.es
Date: Tue Apr 04 2000 - 14:26:13 CDT

Hi,
I have intended to create a DNA duplex with a modification by using LeAP. I have composed a new residue using INSIGHT and Ihave loaded it into xleap. Briefly, I have a library of OFF files coming from pdb separated residues. I load it into xleap.
Then I load a duplex DNA decamer as a pdb file. In this file I have specified, in the proper column, the name of the strange residue ( a modified base in position 8) as follows:

ATOM 138 O2 T 7 -3.563 0.745 20.100 1.00 0.00 O
ATOM 139 N1 T 7 -3.515 3.013 19.860 1.00 0.00 N
ATOM 140 C6 T 7 -2.780 4.168 19.760 1.00 0.00 C
ATOM 141 C5 T 7 -1.434 4.139 19.810 1.00 0.00 C
ATOM 142 C7 T 7 -0.583 5.369 19.700 1.00 0.00 C
ATOM 143 P T3M 8 -8.189 3.510 21.580 1.00 0.00 P
ATOM 144 O1P T3M 8 -9.638 3.338 21.800 1.00 0.00 O
ATOM 145 O2P T3M 8 -7.536 4.582 22.370 1.00 0.00 O
ATOM 146 O5' T3M 8 -7.430 2.130 21.830 1.00 0.00 O

.....

What happens is that xleap does not load this residue from the library file that I have previously loaded. It just treats it as if it was a T. I have tried to change the residue name to a single-letter one (for example a X) but this is treated as a strang
residue and only a group of unconnected atoms is created in its place.
I would appreciate annyone who can give me a solution. HOW CAN I SAY TO XLEAP THAT IT HAS TO LOOK FOR THE NEW SPECIFIED RESIDUE IN THE LIBRARY THAT I HAVE PREVIOUSLY LOADED????
Thanks a lot for your answers,
                                        Bals