Dear Amber users,
I am working with MD simulation of DNA systems. I was trying to generate
topology (*.top) file for some selected atoms of the DNA ( few nitrogen and
oxygen of some bases in DNA )that are not connected to each other. Whenever
I try to run the leap with a pdb file containing (only) these atoms ( TER
card inserted), leap automatically add all the other missing atoms. I tried
running leap with commanding out the 'addPdbResMap' in leaprc.ff99bsc0
file, but it failed to generate a correct topology file. Is there any other
way in leap to make such a topology file?. Waiting for your valuable reply.
Thanks in advance
Sincerely
Aneesh
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Received on Mon Jul 23 2012 - 05:30:02 PDT
