Hi Amber folk,
After running a pmemd.cuda simulation on a normal protein prepared with tleap and leaprc.ff10, I tried to run a PBSA calculation with inp=2 using sander in AMBER 11 with the script on the bottom of this email. However, I got the error,
PB Bomb in pb_aaradi(): No radius assigned for atom 5 CA CX
This had me stuck for a little bit, but then I used leaprc.ff99SB in tleap to generate the prmtop instead. It worked perfectly and I had the same MM energies as with a GB script and the original prmtop.
I am just writing the list to provide a workaround in case somebody else runs into this problem, and also to alert developers to the possibility that PB with inp=2 might not support ff10 atom types with different names than ff99SB (if they don't already know).
Thanks,
David
** Example sander energies given the prmtop based on ff10:
minimizing coord set # 2
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -3.2302E+03 1.9446E+01 1.0836E+02 CG 2052
BOND = 398.8477 ANGLE = 1119.9287 DIHED = 1505.8676
VDWAALS = -1035.4726 EEL = -9542.4883 EGB = -2005.0136
1-4 VDW = 522.2311 1-4 EEL = 5805.9078 RESTRAINT = 0.0000
minimization completed, ENE= -.32301916E+04 RMS= 0.194458E+02
** Example sander energies given the prmtop based on ff99SB
minimizing coord set # 2
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -2.6930E+03 1.9490E+01 1.0846E+02 CG 2052
BOND = 398.8477 ANGLE = 1119.9287 DIHED = 1505.8676
VDWAALS = -1035.4726 EEL = -9542.4883 EPB = -1894.4982
1-4 VDW = 522.2311 1-4 EEL = 5805.9078 RESTRAINT = 0.0000
ECAVITY = 1144.2085 EDISPER = -717.5027
minimization completed, ENE= -.26929704E+04 RMS= 0.194899E+02
** GB script:
Calculate GB energies
&cntrl
imin=5, maxcyc=0, ncyc=0, ! read trajectory in for analysis
ntx=1, ! input is read formatted with no velocities
ntb=0, ! no periodicity and no PME
idecomp=0, ! no decomposition
ntc=2, ! SHAKE
ntf=2, ! omit interactions with H-atoms
cut=1000.0, ! no cutoff (>999.0)
nsnb=99999, ! don't update non-bonded list
temp0=300.0, ! 300 K
igb=5, ! Updated OBC implicit solvent
saltcon=0.025, ! 25 mM salt
ioutfm=1, ! Binary NetCDF output
/
** PBSA script:
Calculate Poisson-Boltzmann energies
&cntrl
imin=5, maxcyc=0, ncyc=0, ! read trajectory in for analysis
ntx=1, ! input is read formatted with no velocities
ntb=0, ! no periodicity and no PME
idecomp=0, ! no decomposition
ntc=2, ! SHAKE
ntf=2, ! omit interactions with H-atoms
cut=1000.0, ! no cutoff (>999.0)
nsnb=99999, ! don't update non-bonded list
temp0=300.0, ! 300 K
ipb=2, ! PBSA
inp=2, ! Two terms for nonpolar solvation energy
ioutfm=1, ! Binary NetCDF output
/
&pb
istrng=25, ! 25 mM salt
pbtemp=300.0, ! 300 K
epsout=80.0, epsin=1.0,
radiopt=1, ! use radii (missing parameter from terminal residue?)
dprob=1.6,
space=0.5, nbuffer=0, fillratio=4.0,
accept=0.001,
cutnb=0, eneopt=2,
decompopt=2, ! sigma decomposition scheme (Luo's paper)
use_rmin=1, ! use van der Waals rmin values
sprob=0.557, ! recommended for sigma decomposition scheme
vprob=1.300,
rhow_effect=1.129, ! recommended for sigma decomposition scheme
use_sav=1, ! use molecular volume enclosed by SASA
cavity_surften=0.0378, ! recommended by Luo
cavity_offset=-0.5692, ! recommended by Luo
/
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Received on Sat Mar 17 2012 - 11:30:03 PDT
