Hello,
Do you have any better insight on how I can define the 1-4 EEL and 1-4 VDW
scale factors so I can run PBSA calculations on my protein system? The
protein membrane system was built in CHARMM-GUI and the CHARMM force field
but simulated using AMBER.
If I set my radii to mbondi with parmed.py and set scnb and scee to 1. I
can get MMPBSA to run this way using sander, but after doing my
subtractions I get extremely positive values like 1200 to 1700. Wondering
if there is a more appropriate way to do this..
Thanks,
-------------------------------------------------------
Amber 18 SANDER 2018
-------------------------------------------------------
| Run on 03/12/2021 at 18:33:29
| Executable path: sander
| Working directory: /home/cad234/projects/NET/net-oocc/test
| Hostname: Unknown
[-O]verwriting output
File Assignments:
| MDIN: mmpbsa.in
| MDOUT: mmpbsa_c.out
|INPCRD:
rstfiles/complex.1
| PARM:
com.prmtop
|RESTRT: restrt
| REFC:
refc
| MDVEL:
mdvel
| MDFRC:
mdfrc
| MDEN:
mden
| MDCRD:
mdcrd
|MDINFO:
mdinfo
| MTMD:
mtmd
|INPDIP:
inpdip
|RSTDIP:
rstdip
|INPTRA: inptraj
Here is the input file:
initial minimization w/ position restraints on DNA, 9.0
cut
&cntrl
imin = 1, ntx = 1, ipb = 2, inp =
2,
/
&pb
epsout=80.0, epsin=1.0,
fillratio=2.0,
radiopt =
0,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
|
Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 03/12/21 Time = 18:33:12
NATOM = 10023 NTYPES = 33 NBONH = 5009 MBONA = 5174
NTHETH = 11330 MTHETA = 7050 NPHIH = 18919 MPHIA = 13049
NHPARM = 0 NPARM = 0 NNB = 55551 NRES = 630
NBONA = 5174 NTHETA = 7050 NPHIA = 13049 NUMBND = 72
NUMANG = 168 NPTRA = 390 NATYP = 0 NPHB = 0
IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Force field information read from topology file:
| CHARMM36 All-atom Force
Field
|
|CHARMM: CHARMM force field in use.
|CHARMM: Overriding default value of chngmask.
|CHARMM: Setting chngmask = 0.
| Memory Use Allocated
| Real 857029
| Hollerith 30701
| Integer 517961
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 8838 kbytes
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
ERROR: Flag "RADII" not found in PARM file
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Received on Sat Mar 13 2021 - 10:00:02 PST
