Hello Dr. Pengfei Li,
Sorry for the late reply, I just read this conversation.
I also want to simulate Hydroxyapatite, and follow this Tutorial:
https://ambermd.org/tutorials/advanced/tutorial27/hap_water.php
But when I tried to run this line: tleap -s -f hap_tleap.in > hap_tleap.out
it was an error.
Then I open file hap_tleap.in and I found this command "source
leaprc.interface_v1_5" in the first line.
I think this is the problem.
Then I try to look in to folder $AMBERHOME/dat/leap/cmd, there no file
for leaprc.interface_v1_5.
The I download Interface-MD Force Field in this Web site :
https://bionanostructures.com/interface-md/.
I extracted and found the list of forcefield is
charmm27_interface_v1_5.prm
cvff_interface_v1_5.frc
cvff_interface_v1_5_templates.dat
pcff_interface_v1_5.frc
pcff_interface_v1_5.off
pcff_interface_v1_5_templates.dat
Do we have to convert one of the FF into leaprc.interface_v1_5 ?
Or do you have any suggestions?
Thank you
-------
Setyanto Tri Wahyudi
-------
Computational Biophysics Group,
Department of Physics, IPB University - Indonesia
Gedung Fisika Wing-S Lt.2 Jl. Meranti
Kampus IPB Darmaga
Bogor - 16680
Indonesia
On Wed, May 31, 2017 at 12:40 AM Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> Hi Sohag,
>
> I have no problem to load the lib file. There may be some issues with your
> LEaP. You can go to “$AMBERHOME/AmberTools/test/leap” to test its
> installation.
>
> Kind regards,
> Pengfei
>
> > On May 29, 2017, at 11:24 PM, Sohag Biswas <cy13p1001.iith.ac.in> wrote:
> >
> > Dear all amber users,
> > I want to simulate a peptide on Ag fcc surface and I have following the
> > AMBER advanced tutorial 27. After executing all the command, at the end
> it
> > is showing fcc_metals.lib is not a valid database. I have downloaded all
> > the parameters file from amber website. Is there any modification
> required
> > in any file like, leaprc.interface_v1_5 or interface_v1_5.dat ? Any
> > suggestions will be highly appreciated.
> >
> > Thank you so much :)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Nov 11 2023 - 19:00:04 PST
