AMBER Archive (2005)

Subject: Re: AMBER: fail of minimization in sander

From: Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Stefano.Pieraccini_at_unimi.it)
Date: Wed Jun 15 2005 - 06:05:25 CDT

Dear Wendy,

the problem you reported is due to the compilation of amber, that was
customed in a way that is not able to deal with the 10-12 coefficients
you introduced in you parm file. You should recompile at least sander
inserting in your MACHINE file, located in the directory amber7/src,
the line

setenv MACHINEFLAGS "-DHAS_10_12"

and then recompile the program. This line only allow to recompile amber
in a way so it can recognise this coefficients for short range
interactions if present in the file you submit.

Stefano Pieraccini

> I try to get the output file by using one of my friends' single
> PC. The
> output file is listed below. It seems that the way I form my
> ".inpcrd"and
> ".prmtop" file by modifing the Amber parameters cause the
> minimization
> problem. Would you give me some suggestions?
>
> ps: There are a platinum atom in my molecule. And that is why I
> have modify
> the Amber parameters.
>
> Thank you!
>
>
> -------------------------------------------------------------------
> -------------
> 1. RESOURCE USE:
> -------------------------------------------------------------------
> -------------
>
> | Flags:
> | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
> | *** cutoff > system size, list only builds once
> |Largest sphere to fit in unit cell has radius = 42.215
> | New format PARM file being parsed.
> | Version = 1.000 Date = 05/25/05 Time = 13:57:45
> NATOM = 767 NTYPES = 26 NBONH = 278 MBONA = 548
> NTHETH = 652 MTHETA = 846 NPHIH = 1262 MPHIA = 1492
> NHPARM = 0 NPARM = 0 NNB = 4282 NRES = 25
> NBONA = 548 NTHETA = 846 NPHIA = 1492 NUMBND = 47
> NUMANG = 100 NPTRA = 52 NATYP = 31 NPHB = 24
> IFBOX = 0 NMXRS = 34 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
>
> | Memory Use Allocated
> | Real 61986
> | Hollerith 4629
> | Integer 1555072
> | Max Pairs 293761
> | Max Rstack 57670
> | Max Istack 3835
> | Total 8189 kbytes
> Found a non-zero 10-12 coefficient, but source
> was not compiled with -DHAS_10_12.
> If you are using a pre-1994 force field, you
> will need to re-compile with this flag.
>
>
>
> Sincerely,
>
> Wendy
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