Dear amber users,
I am trying to calculate binding free energy of two protein chains. Let me first explain the situation.
I carried the MD simulation with NAMD, then I converted the NAMD trajectory file (.dcd) to the AMBER format (.mdcrd) using VMD. Then I stripped the water molecules and counter ions leaving only the receptor and the ligand naked. Next, I made the neccessary corrections such as residue naming, bonding representation. Finally, I created the topology files using xleap. I was also able to generate the snapshots for the calculations. But when I tried to do stability calculation I encountered some errors in the pbsa_com.1.out file. Here I paste some parts of the file,
| Run on 08/21/2006 at 11:29:37
[-O]verwriting output
File Assignments:
| MDIN: pbsa.in
| MDOUT: pbsa_com.1.out
|INPCRD: /root/Desktop/comp3/snapshots2/agpase_com.crd.1
| PARM: /root/Desktop/comp3/complex2.prmtop
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
File generated by mm_pbsa.pl. Using PB
&cntrl
ntf = 1, ntb = 0,
igb = 10, dielc = 1.0,
cut = 999.0, nsnb = 99999,
scnb = 2.0, scee = 1.2,
imin = 1, maxcyc = 0, ntmin = 2,
&end
&pb
epsin = 1.0, epsout = 80.0,
istrng = 0, radiopt = 1,
sprob = 1.6, space = 0.5,
maxitn = 500
npbverb= 1
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 08/21/06 Time = 11:09:52
NATOM = 13776 NTYPES = 14 NBONH = 6892 MBONA = 7023
NTHETH = 15697 MTHETA = 9508 NPHIH = 29416 MPHIA = 20490
NHPARM = 0 NPARM = 0 NNB = 76179 NRES = 883
NBONA = 7023 NTHETA = 9508 NPHIA = 20490 NUMBND = 42
NUMANG = 92 NPTRA = 47 NATYP = 29 NPHB = 0
IFBOX = 0 NMXRS = 26 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 510170
| Hollerith 83541
| Integer 704318
| Max Pairs 1
| Max Rstack 1
| Max Istack 1
| Total 7063 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
total system charge for PB -10.0000010237676
SAS Surface: setting up working radii
SAS Surface: found nonzero radii 10300
SAS Surface: surface dots generated: 366
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
TITLE : Created by VMD with 105289 atoms
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NB-update: residue-based nb list 6213107
NB-update: atom-based nb list 1529580
======== Setting up Grid Parameters ========
Using bounding box for grid setup
Bounding Box Center: 31.784 8.992 51.169
Xmin, Xmax, Xmax-Xmin: -13.951 77.519 91.470
Ymin, Ymax, Ymax-Ymin: -39.710 57.695 97.405
Zmin, Zmax, Zmax-Zmin: 14.521 87.818 73.297
beginning box center at level 1 31.784 8.992 51.169
beginning box center at level 2 31.784 8.992 51.169
Grid dimension at level 1 47 51 39
Grid origin corrected at level 1 -64.216 -95.007 -28.831
Grid dimension at level 2 199 211 163
Grid origin corrected at level 2 -18.216 -44.008 10.169
Number of SA srf points exposed 103192
PB bomb in pb_saarc(): Allocation aborted 0 41 41
My first question is about the meaning of this "Allocation aborted" error, what does that mean?
The second question is that whether I should worry about the "Number of triangulated 3-point waters found: 0" output in the third part, since I used an explicit solvent system during the simulation.
The last question is that, altough I solvated my system in a water box the .prmtop file does not contain any box info. Should I include the box info into the .prmtop file for the calculations, if yes how?
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Received on Wed Aug 23 2006 - 06:07:09 PDT
