I am attaching the PDB. Force field is ff10 and Amber version is 11. And i
just loaded tleap sourcing ff10, after that i gave this command :
loadamberparams frcmod.ionsjc_tip3p
m=loadpdb test.pdb
Following which i got this message. There are some atoms displaying
alternative conformations. I have not removed them.
PDB format versions of the file also looks compatible with ff10: "REMARK
4 1L2X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08"
Asmi
On Tue, May 15, 2012 at 1:48 PM, case <case.biomaps.rutgers.edu> wrote:
> On Tue, May 15, 2012, Asmita Gupta wrote:
> >
> > I have a PDB file of RNA crystal structure.
> >
> > Unknown residue: C number: 0 type: Terminal/beginning
> > ..relaxing end constraints to try for a dbase match
> > -no luck
> > Unknown residue: G number: 1 type: Nonterminal
>
> We need to know what your pdb file looks like (at least for the first
> couple
> of residues), and, more importantly, what force field and Amber version you
> are loading, that is, exactly which commands you gave to LEaP. You should
> be using either ff10 or ff12SB to smoothly read PDB files that conform to
> PDB
> format 3.x.
>
> ....dac
>
>
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Received on Tue May 15 2012 - 02:00:05 PDT
