On Tue, May 15, 2012, Asmita Gupta wrote:
> 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.
> > >
> > > 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
I cannot reproduce the problem. Here is exactly what I did:
tleap -f leaprc.ff10
> x = loadpdb test.pdb
result:
> x = loadpdb test.pdb
Loading PDB file: ./test.pdb
-- residue 10: duplicate [ O3'] atoms (total 2)
-- residue 11: duplicate [ C1'] atoms (total 2)
-- residue 11: duplicate [ C2] atoms (total 2)
....(similar lines deleted)
Warning: Atom names in each residue should be unique.
(Same-name atoms are handled by using the first
occurrence and by ignoring the rest.
Frequently duplicate atom names stem from alternate
conformations in the PDB file.)
total atoms in file: 641
Leap added 293 missing atoms according to residue templates:
293 H / lone pairs
I'm using the tleap in AmberTools12. If you want the first of the duplicate
atoms, you can ignore the warnings. Otherwise, you would have to manually
edit the PDB file to choose which conformer you want.
Bottom line is that we have to figure out what is different between your
system and mine.
....dac
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Received on Tue May 15 2012 - 03:30:04 PDT
