On Thu, Feb 21, 2013 at 4:12 PM, <moitrayee.mbu.iisc.ernet.in> wrote:
> Dear Amber Users,
>
> I am trying to construct a dipeptide using gamma-amino acid. I have
> obtained the
> parameters using the red server and I use the following script to generate
> the
> prm top and crd files:
>
> GVA=loadmol2 GVA.mol2
> loadamberparams GVA.frcmod
> gva=sequence { GVA GVA }
> solvatebox gva TIP3PBOX 9.00 0.75
> saveamberparm gva gva.prmtop gva.prmcrd
> quit
>
> When I use the same script for VAL, it works but with GVA, it gives TER
> separated units of GVA.
>
> For parameter generation in case of GVA, I have considered the amino acid
> to be
> in the NH-XXXX-CO state. I am a little confused how to go about this and
> would
> very much appreciate any help in this regard.
>
This is because the mol2 file does not have connectivity information. You
need either the OFF file or the mol3 file which has this information.
You need to define the head and tail atom of GVA. So for the VAL amino
acid, something like this:
set VAL head VAL.1.N
set VAL tail VAL.1.C
(Note, this has already been done for the VAL residue, which is why it
'works' for you).
Note that your command is unlikely to 'work'. GVA-GVA implies that GVA has
both a head atom and a tail atom (since that's the only way GVA can bond to
itself in sequence). However, the head of the first GVA and tail of the
second will be dangling (that is, there will be nothing bonded with it).
To demonstrate, this is -wrong-:
valval = sequence {VAL VAL} # Dangling bonds!
this is -right-:
valval = sequence {NVAL CVAL} # N-terminal valine bonded to C-terminal
valine
This is also -right-:
valval = sequence {ACE VAL VAL NME} # valine-valine with neutral caps
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 21 2013 - 14:30:02 PST
