I have used source leaprc.ff99
and this script to generate topology and coordinate file
echo com = loadpdb $1".pdb" > leap.in
echo loadamberparams frcmod.tip4pew >> leap.in
echo solvateoct com TIP4PEWBOX 11.0 >> leap.in
echo addions com Na+ 0 >> leap.in
echo saveamberparm com $1"_wat.top" $1"_wat.crd" >> leap.in
echo quit >> leap.in
tleap -f leap.in
I didn't derive any forcefield for any residue.
Thanks and regards
Ashutosh Shandilya
On 4 June 2010 23:04, Gustavo Seabra <gustavo.seabra.gmail.com> wrote:
> On Jun 4, 2010, at 1:45 PM, ashutosh shandilya wrote:
>
> > In context of my previous mail the helix is getting unfolded and
> sometimes
> > sheets are disappearing as well because of 2.1ns md simulation in water
> at
> > constant pressure.Which structure shall I take and the reason for
> unfolding.
> > Thanks and regards
> > Ashutosh Shandilya
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
> Adding to Bill's suggestion, it would also help to know which force
> fields are you using. did you have to derive force fields for any
> residue?
>
> Gustavo.
> --
> Sent from my iPad
>
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Received on Fri Jun 04 2010 - 11:00:08 PDT
