VMD-L Mailing List

From: Moumita Maiti (m.moumita_at_gmail.com)
Date: Wed Jun 14 2006 - 06:13:20 CDT

Hi,

          I am trying to generate a psf file which contains nine segments,
where two of them are DNA. I tried to
run psfgen through vmd, then I get the following warnings,

Can anybody help me so that I can get rid of these warnings?

Info: generating structure...
Info: skipping conformation O3'-O5'-P-O2P at beginning of segment.
Info: skipping conformation O3'-O5'-P-O1P at beginning of segment.
Info: skipping conformation O3'-P-O5'-C5' at beginning of segment.
Info: skipping bond O3'-P at end of segment.
Info: skipping conformation C3'-O3'-P-O5' at end of segment.
Info: skipping conformation C4'-C3'-O3'-P at end of segment.
no atom C in residue THY:-72 of segment DN0
Warning: add conformation failed in patch NTER
no atom CA in residue THY:73 of segment DN0
Warning: add improper failed in patch CTER
no atom CA in residue THY:73 of segment DN0
Warning: add conformation failed in patch CTER
no atom N in residue THY:73 of segment DN0
Warning: add conformation failed in patch CTER

Regards,
moumita