[AMBER] Fwd: PB with inp=2 doesn't recognize ff10 atom types?

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Sat, 17 Mar 2012 19:33:14 -0700

I'm forwarding this to Qin for an answer ...

Ray


---------- Forwarded message ----------
From: David Minh <daveminh.gmail.com>
Date: Sat, Mar 17, 2012 at 11:10 AM
Subject: [AMBER] PB with inp=2 doesn't recognize ff10 atom types?
To: AMBER Mailing List <amber.ambermd.org>


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 - 20:00:02 PDT
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