Dear Amberians,
We are trying to construct an Au-S-(CH2)6-SH system topology file in Amber.
We used Chem3D pro to make a mol2 file. We are trying to use this mol2 file
to generate the topology files using antechamber. While following the
antechamber tutorial, I was using the Parmchk to generate the frcmod file
to generate missing parameters.
So, here comes my problem.
1)The command is giving segmentation fault. When I looked at my mol2 file
the atom name is not in the same format that are recognized by amber(in
PARMCHK.dat file) so I changed the atom name for C and S.Now the problem
lies that in the PARMCHK.dat file there is nothing for gold. So the command
still gives following error-
"Warning: Atom type (Au) is not in PARMCHK.DAT; using default values
for improper_flag [0], group_id [0], and equivalent_flag [0].
Warning: No mass information for atom type (Au); set to 0.0.
It is recommended to add the new atom type (Au) to PARMCHK.DAT.
Segmentation fault (core dumped)"
P.S. -We have set up a simulation with gold using the interface forcefield
extension before and that we would like to use the parameters from there.
Thanks a lot in advance for any suggestions or hints.
*Anirudh Mantri *
Department of Biotechnology
Indian Institute of Technology Kharagpur
Phone: +91-89420 49025
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Received on Mon Jun 08 2020 - 02:00:02 PDT
