AMBER Archive (2004)

Subject: AMBER: mm_pbsa

From: Carsten Detering (detering_at_u.washington.edu)
Date: Wed Dec 15 2004 - 15:57:13 CST

Dear Ambers,

I am trying to calculate the binding free energies of a receptor-ligand
system. I have done MD calculations of receptor, complex and ligand and
had run the mm_pbsa script. THis crashed with the error message

Use of initialized value in multiplication (*) at mm_pbsa_statistics.pm
in line xxxx.

In a reply to a similar question Holger suggested to uncomment an unlink
line respectively lines that remove log files in functions calc_ms and
calc_MM_GB_SAS in mm_pbsa.pl. However, I couldnt find these lines in
mm_pbsa.pl, nor in mm_pbsa_statistics.pm or .pl.
Also, in my snapshot_com.all.out file, I have extremely high values for
bond, vdwaals:

1
  BOND= ************* ANGLE= 421069.8333 DIHED = 15394.0843
  VDWAALS = 23370405.3369 EEL=-5623.0283 EGB = -11077.6051
  1-4 VDW =6469138.6972 1-4 EEL =-1616.4403 RESTRAINT = 0.0000
surface area = 32572.258
2
  BOND= ************* ANGLE = 436342.1221 DIHED = 15252.8323
  VDWAALS = 21796995.3503 EEL = -7317.9479 EGB = -12240.0119
  1-4 VDW = 7685667.6996 1-4 EEL = -2100.5084 RESTRAINT = 0.0000
surface area = 48380.357
3
  BOND= ************* ANGLE= 440782.5227 DIHED= 15182.4016
  VDWAALS = 38617083.1465 EEL =-5522.8243 EGB = -14408.3222
  1-4 VDW = 8306575.3731 1-4 EEL =-2875.8035 RESTRAINT = 0.0000
surface area = 62944.652

Here is what I did in the preceeding md simulation:
I set the pbradii to mbondi, i used ntt=1 for the production run, but
ntt=3 for equilibration.
THis was the last mdinfo from the complex production run in the
preceeding md simulation:

NSTEP =250000 TIME(PS) = 960.000 TEMP(K) = 301.51 PRESS = 424.2
  Etot = -79503.7791 EKtot= 19737.1146 EPtot = -99240.8937
  BOND = 800.8894 ANGLE = 2288.5429 DIHED = 2960.6663
  1-4 NB = 1222.1709 1-4 EEL = 7860.3877 VDWAALS = 10098.5623
  EELEC = -124472.1131 EHBOND= 0.0000 RESTRAINT = 0.0000
  EKCMT = 8270.3975 VIRIAL = 5379.9569 VOLUME = 315615.1504
                                            Density = 1.0323
  Ewald error estimate: 0.2406E-04

What could be the reason for the bond and van der waals values being so
high for mm_pbsa?
And how do I solve the problem with the uninitialized values?

Every suggestion will be greatly appreciated!

Thanks a lot in advance,

Carsten
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