Then it is perhaps not 5'AMP you have? 3'AMP is generated with appropriate FIRST and LAST patches specified to the GENErate command (5TER, 3PHO); see the topology (RTF).
Still I suppose you could start from 5'AMP/3'AMP and add your extra atoms. Note that you probalby also need to patch it, after the GENErate, to be a deoxyribose and that the generate command may need a "LAST 3TER".

The commands are standard CHARMM commands for generating a "PSF". See examples in the Script Archive forum, the CHARMM doucmentation and the CHARMM Course forum as well as tutorials available under LINKS on www.charmm.org.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden