Dear Amber Users,
I want to simulate a nucleic acid system, which have crystal structure in
RCSB. The crystal structure contains Mn2+, Mg2+ and crystal water.
I found that there is parameter for Mg2+ in
amber(amber12/dat/leap/lib/ions94.lib). But no parameter for Mn2+. How to
get and load the Mn2+ parameter.
I want to put those crystal waters and ions as they in the PDB file. Can I
allow the waters in the input pdb file. In presence of these waters and
ions the tleap message is as follows:
Starting new chain with MG2
Starting new chain with MG2
Creating new UNIT for residue: MN sequence: 12
Starting new chain with
Created a new atom named: MN within residue: .R<MN 12>
Starting new chain with TP3
Starting new chain with TP3
Starting new chain with TP3
Starting new chain with TP3
Starting new chain with TP3
Starting new chain with TP3
My questions are:
1. Is it working with crystal waters ?
2. Is it working with the Mg2+
3. How to get the Mn2+ parameters ?
Thanks
---indrajit
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Indrajit Deb
Kolkata, India.
Mob: +919239202278
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Received on Sat Jun 23 2012 - 13:00:03 PDT
