Parameterisation of Metallo-protein with amber
0
0
Entering edit mode
2.6 years ago

Hello guys!

Can someone please help me with a protocol for parameterizing a metallo-protein for MD simulation with amber forcefield? My protein has two FE molecules and the I tried using either frcmod.ionsjc_tip3p or frcmod.ions234lm_126_spce to generate topology but the system is not minimizing. I confirmed that there are no atomic clashes in my system, so I guess the problem has to do with the ions parameters.

Metallo-protein Amber MD ion simulation FE • 502 views
ADD COMMENT
1
Entering edit mode

You could try to use gromacs.

ADD REPLY

Login before adding your answer.

Traffic: 2211 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6