Hi Kurisaki,
> > Annomalous "TER" is sometime inserted between standard and Non-standard
one in PDB formatted file.
(ambpdb or savepdb?) This same problem I usually get when I deal with non
standard residues. You may like to follow suggestion provided below. And if
you use pdb files having undesired TER cards and using that you are saving
prmtop file then AMBER will take the residues being non-bonded. So you need
to remove the undesired TER cards if you want to use the pdb so that AMBER
knows that all residues are bonded. ALSO sometimes (again this occurs when
I am using non-standard residues ) you need to use bondbydistance command
in such case even if you remove TER cards in pdb file otherwise while
saving pdb file AMBER will not consider residues as bonded. But this
creates another problem because if you are loading PDB (not minimized) and
using bondbydistance then you may get extra undesired bonds between close
atoms. Which is an anomaly. TO overcome this you can use strategy as
follows:
Here are some suggestions:
Just after using sequence command (after all the amino acids have been
joined), you can save a prmtop and inpcrd file and create mol2 using
top2mol2
e.g x = sequence {a b c d ....}
saveamberparm x x.prmtop x.inpcrd
quit
top2mol2 -p x.prmtop -c x.inpcrd -at amber -o x.mol2
This x.mol2 is directly loadable in xleap/tleap (later you can add ions
water etc.) and it contains atom types in extra column (and yes you have to
source force field you are using). Most importantly it has bond information
and thus you need not to worry about above said issues with PDB.
regards,
On Tue, Mar 5, 2013 at 2:36 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Mar 05, 2013, kurisaki wrote:
> >
> > When I build an poly-peptide including non-standard amino acid (AA),
> > Annomalous "TER" is sometime inserted between standard and
> > Non-standard one in PDB formatted file.
>
> You don't say how you created the PDB-format file. Try ambpdb: it places a
> TER card between adjacent residues if there are no bonds between them. If
> you
> get an unwanted TER card, you need to check your bond list carefully. (You
> should probably check the bond list anyway if you are using a non-standard
> amino acid, to make sure you are getting what you want.)
>
> [I'm not sure off-hand how LEaP decides where to put TER cards.]
>
> ....dac
>
>
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>
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Vishal Maingi*
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Received on Tue Mar 05 2013 - 05:00:03 PST
