Dear N Nandi,
> We attach an text file which will describe the whole thing. We
> actually want to load the whole tRNA molecule without making any
> change and then we want to calculate the ESP potential map using
> PBSA.
-----
> loadoff tRNA.lib
Loading library: ./tRNA.lib
Bond: Maximum coordination exceeded on A<H5T 36>
-- setting atoms pert=true overrides default limits
> x=loadpdb 6TNA.pdb
Loading PDB file: ./6TNA.pdb
Created a new atom named: OP1 within residue: .R<RG5 1>
Created a new atom named: OP2 within residue: .R<RG5 1>
Created a new atom named: OP3 within residue: .R<RG5 1>
Created a new atom named: P within residue: .R<RG5 1>
-> this means tRNA.lib is not compatible with 6TNA.pdb: however as we
do not know what is in "tRNA.lib" we cannot help...
As a general rule the atom & residue names in the PDB file have to
match these in the FF lib.
Two other comments:
- [root.localhost bin]
do you run LEaP as a superuser (root)? I think this is a bad idea; you
could install AMBER as the superuser; but you should use it from your
personal login (just define $AMBERHOME & $PATH in your .bashrc or
.cshrc file).
- [root.localhost amber11]# cd $AMBERHOME
[root.localhost amber11]# cd exe
I would not run LEaP from the $AMBERHOME/exe directory but from a
directory in my personal login. For instance in our cluster AMBER is
installed in /usr/local and I use/call it from my personal login
/home/fyd.
regards, Francois
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Received on Mon Apr 08 2013 - 01:00:08 PDT
