Note also, top2mol2 while writting mol2 file adds residue number after
residue name also: e.g.
1 C1 -5.7049 2.0430 -1.8914 c3 1 XYZ1 0.0988
CORRECT it to be as:
1 C1 -5.7049 2.0430 -1.8914 c3 1 XYZ 0.0988
regards,
On Tue, Mar 5, 2013 at 2:54 PM, Vishal Maingi <maingi.ambquery.gmail.com>wrote:
> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> *****
> *regards;
> Vishal Maingi*
> *Dendrimer Builder Toolkit (DBT)*
> \I/
> >-|-<
> /I\*
> *
> *http://www.physics.iisc.ernet.in/~maiti/dbt/home.html*
> *****
>
--
*****
*regards;
Vishal Maingi*
*Dendrimer Builder Toolkit (DBT)*
\I/
>-|-<
/I\*
*
*http://www.physics.iisc.ernet.in/~maiti/dbt/home.html*
*****
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Received on Tue Mar 05 2013 - 05:30:03 PST
