Dear Amber users,
I was generating DNA with 20 pairs (40 residues) using NUCGEN, but I can
generate only 16 pairs (32 residues). When I looked in source code of
nucgen.f in $AMBERHOME/src/etc directory, it seems that nucgen is limited to
16 pairs (I am not sure because I have no more experience in writting
program e.g. fortran). I have changed a number from 16 to 20, and changed
some reading format. Then I recompiled nucgen again. Now I can generate DNA
with 20 pairs. However, I am not sure that this is a good way to solve
problem. Could anyone please suggest me another method to generate DNA more
than 16 pairs?
Another question is that I have worked with 10 pairs DNA following by
tutorial in AMBER web site. In the adding solent step (using tleap), DNA was
solvated with WATBOX216 of 10.0 angstrom in each direction. Everything was
good. Now I am working with 20 pairs DNA. Could you please suggest me that
how distance of adding WATBOX216 should be added?
Thank you very much in advance.
Xiaolin
_________________________________________________________________________
Get Your Private, Free E-mail from MSN Hotmail at
http://www.rosswalker.co.uk/adsense_alternatives/.
Received on Thu Jul 05 2001 - 05:06:39 PDT
