[AMBER] problem with type of pdb output.

From: lawrence awadetsi <lorenskobb.googlemail.com>
Date: Tue, 12 Jul 2011 22:07:33 +0400

i did this with nab.
*molecule m;
m = bdna("tatatatatatatatatatatatatatatatata");
*
*putpdb("ta_34.pdb", m);*



the output:

ATOM 1 HO5' DT5 A 1 -0.443 -8.367 -1.903 1.00 0.00

ATOM 2 O5' DT5 A 1 0.401 -8.012 -1.614 1.00 0.00

ATOM 3 C5' DT5 A 1 1.429 -7.769 -2.593 1.00 0.00 ......

i had wanted the form of pdb file to contain "EIC" instead of "DT5, etc" in
the corresponding column. how do i do that cos i want to use the output file
in "antechamber" to do something like this:


*antechamber -i eic_clean1.pdb -fi pdb -o eic_clean1.mol2 -fo mol2 -c bcc -s
2
*
*parmchk -i eic_clean1.mol2 -f mol2 -o eic_clean1.frcmod*

thank you.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 12 2011 - 11:30:02 PDT
Custom Search