Hi all,
I found my mistake, I just wanted to share this. It seems I had a bad gaff names in mi ligand.mol2. I use ca instead c3, and obviously my structure collapsed. Thats it
Bests
Cesar
________________________________
From: MENDOZA Cesar <Cesar.Mendoza.ed.ac.uk>
Sent: 23 January 2020 15:23
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: About ions coordinated to Zinc
Hi all,
I successfully made the coordination compound which has attached two chlorine and two organic molecules to Zinc in a tetrahedral configuration using MCPB.py. When I tried to minimize the system (successfully) and then heat the all system, in the last step I got next error,
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 4 6 39 40
Note: This is usually a symptom of some deeper problem with the energetics of the system
I was wondering if I need to heat the system gently or if this might because the parametrization doesnt describe correctly the coordination. I was wondering also, if this is because the geometry changes and it cause a trouble similar like in water but here because Chlorine. Do you think I need to use a non-bonded model? I was thinking using to use EZAFF for Zn but I cannot find a proper tutorial. Nezt system I need to work with contains a ferrocene. Is it possible to parametrize this molecules using MCPB.py?
My inputs are
1. Minimise whole system
&cntrl
imin = 1, ntmin = 1,
maxcyc = 1000, ncyc = 10,
ntpr = 200, ntwe = 200,
dx0 = 1.0D-7,
ntxo = 1, ! 2 is default in AMBER16 for NetCDF file
ntb = 1,
ntr = 1, restraint_wt = 10.00,
restraintmask="!:WAT,HOH,T3P,T4P",
/
2. heat the system
&cntrl
imin = 0, nstlim = 1000, irest = 0, ntx = 1, dt = 0.002,
nmropt = 1,
ntt = 1, temp0 = 300.0, tempi = 5.0, tautp = 1.0,
ntb = 1, pres0 = 1.0,
ntc = 2, ntf = 2,
ioutfm = 1, iwrap = 1,
ntxo = 1, ! 2 is default in AMBER16 for NetCDF file
ntwe = 200, ntwx = 200, ntpr = 100,
ntr = 1, restraint_wt = 10.00,
restraintmask="!:WAT,HOH,T3P,T4P",
/
&wt
type = 'TEMP0',
istep1 = 0, istep2 = 1000,
value1 = 5.0, value2 = 300.0
/
&wt type = 'END'
/
Best wishes
Cesar Mendoza
________________________________
From: MENDOZA Cesar
Sent: 20 January 2020 14:45
To: amber.ambermd.org <amber.ambermd.org>
Subject: About ions coordinated to Zinc
Hi All,
This is my first attempt to parametrize a 4 coordinated complex with Zinc by using MCPBY.py tool. I have tried but it seems there are some issues. I was wondering if someone have used contra ions *like Cl-, F- or Br-) as part of the coordination sphere, and how you threat this on the setup.in, as ion_mol2files or naa_mol2files?.
Best wishes
Cesar
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 24 2020 - 15:30:02 PST
