AMBER Archive (2006)

Subject: AMBER: nmode memory allocation error

Date: Fri Sep 08 2006 - 03:41:35 CDT

Dear Amber users,

I am trying to calculate binding free energy of a protein complex composed of 6874 and 6902 atoms (with hydrogens) for corresponding ligand and receptor chains using MMPBSA method with Amber8. When I try to make nmode calculation the program gives the following error message after sander minimization,

/home/atuncel/amber8/exe/nmode -O -i -o nmode_lig.1.out -c\ sanmin_lig.1.restrt -p /home/atuncel/energy/SS_A+LS_B/SS_A.prmtop not running \properly

and in the nmode_lig.1.out file it says,

 File generated by \
       ntrun maxcyc ibelly drms
          1 100 0 0.10E+00
       rcut scnb scee dielc idiel
     99.00000 2.00000 1.20000 4.00000 0
      nsave dfpred bdwnhl smx emx alpha ndiag
         20 0.01000 0.10000 0.08000 0.30000 0.80000 10
 ipol = 0
 i3bod = 0
 nvect = 0
     Binary format used for input coords.
| New format PARM file being parsed.
| Version = 1.000 Date = 08/24/06 Time = 11:20:47

    PARM file has the title:

Total memory required : 638255263 real words

Total memory required : 24068644 integer words

Maximum nonbond pairs 23622500
ASSERTion 'ier == 0' failed in nmode.f at line 105.

I am aware that this is a memory allocation problem and I need ~5,1 GB memory. The thing is I used 8 parallel Pentium 4, 2.4 Ghz, 1Gb memory machines.

Here are my questions,

1) Is this source of memory not enough or is it possible to make the calculations if I increase the memory?

2) Before the calculations I made the following changes during installation,
i)changed the MAXAT in molsurf.h to 20000 atoms
ii)changed to single precision using pb_def.h file
iii)changed the parameters in sizes2.h file as follows;

parameter (memdrv=10000000)
parameter (maxatom=15000)
parameter (maxint=500)
parameter (maxvec=500)
parameter (maxdih = 5500000000)
parameter (maxdia = 3500000000)
parameter (maxinb = 9000000000)
parameter (maxbon = 2600000000)
parameter (maxbnh = 2000000000)
parameter (maxang = 3000000000)
parameter (maxanh = 3000000000)

Can the error be somehow related to these modifications ?

3) I know that nmode calculations are very difficult for such big systems,can it be appropirate if I use the ismem option in NMODE, otherwise I will have to decrease the number of atoms by just taking the binding domains into account for the calculations.

Thanks in advance.


ps: attached is my sanmin_lig.1.out

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