AMBER Archive (2004)

Subject: Re: AMBER: nucgen problem

Date: Thu Nov 25 2004 - 03:04:28 CST

Did you really want T's in your RNA? If so, nucgen may well not have
parameters for that.

David Evans
School of Pharmacy, University of London

---- Message from at 2004-11-24 17:08:52 ------ >Dear Amber Community, > >I am just starting to work with nucgen as it was supplied with Amber7. >The problem I am encountering is this. When inputting the following: > NUC1 >R >C5 G C A A A T T T G G G3 > > NUC2 >R >G5 C G T T T A A A C C C3 > >END >$ARNA > >The out file says everything is fine: > > ------------------------------------------------------ > Amber 5 NUCGEN UCSF 1997 > ------------------------------------------------------ > > INPUT MOLECULES INFORMATION > > NUC1 > > MOLECULE 1 CONTAINS 12 RESIDUES: > > C5 G C A A A T T T G G G3 > NUC2 > > MOLECULE 2 CONTAINS 12 RESIDUES: > > G5 C G T T T A A A C C C3 > New (1994) residue naming convention > > GENERATING RIGHT HANDED A-RNA(ARNOTT) > > reading monomer parameters > >Put when I open the pdb and look at it, the T bases are not there. The >geometry file (ngdat) is the one that was supplied with the program. I >have attached the pdb file generated by nucgen. Does anybody know why >this happens and how I would resolve this? > >Best Regards, > >Armin > > > > ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to