AMBER Archive (2004)

Subject: Re: AMBER: Problem using GLYCAM with sander

From: Bimo Ario Tejo (bimo7_at_gmx.de)
Date: Sat Jan 24 2004 - 09:28:15 CST

...just remove HBOND information from your glycam parm file.

regards,
bimo

> Dear Amber users
>
> I am trying to use Glycam for the study of carbohydrates.
> I load the last version of the glycam force fiel, I builded the topology
> and coordinates files with Leap, and when I try to minimize my structure
> with Sander
> I have the following error message in the output file:
>
>
--------------------------------------------------------------------------------
>
> 1. RESOURCE USE:
>
--------------------------------------------------------------------------------
>
> | Flags: MEM_ALLOC
> | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
> | New format PARM file being parsed.
> | Version = 1.000 Date = 01/22/04 Time = 08:45:10
> NATOM = 294 NTYPES = 8 NBONH = 140 MBONA = 168
> NTHETH = 322 MTHETA = 252 NPHIH = 616 MPHIA = 601
> NHPARM = 0 NPARM = 0 NNB = 1779 NRES = 14
> NBONA = 168 NTHETA = 252 NPHIA = 601 NUMBND = 10
> NUMANG = 21 NPTRA = 22 NATYP = 8 NPHB = 1
> IFBOX = 0 NMXRS = 21 IFCAP = 0 NEXTRA = 0
>
>
> | Memory Use Allocated
> | Real 24078
> | Hollerith 1780
> | Integer 613606
> | Max Pairs 43071
> | Max Rstack 2000000
> | Max Istack 2000000
> 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.
>
> Here is my input file:
>
> #optimization
> &cntrl
> imin = 1,
> maxcyc = 10000, ncyc = 5000,
> ntx = 1,
> scee = 1.0, scnb= 1.0,
> ntb = 0, igb = 0,
> &end
>
> Could someone explain me what does it mean? If I am not wrong, the new
> version of glycam is not a pre-1994 force field.
> How can I solve this problem?
>
> Thanks very much in advance
>
>
> Itziar Maestre
>
>
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