Dear Prem Raj,
You need to modify the machine file ./amber/src/MACHINE which should be
a symbolic link to the machine file that is relevant to your system, e.g
Machine.g77.
In this file you should find a line similar to:
Setenv MACHINEFLAGS "-DISTAR2 -DREGNML -DMPI"
Simply change the "-DISTAR2" to "-DISTAR4" which will change the
relevant integers from 16 bits to 32 bits which should be good for 2^31
atoms. Plenty :-)
You then need to recompile by running "make install" within the amber
src directory.
All the best
Ross
/\
\/
|\oss Walker
| Imperial College of Science, Technology & Medicine |
| Department of Chemistry | Theoretical Division |
| Tel:- +44 20 759(45851) |
| EMail:-
http://www.rosswalker.co.uk/ |
| PGP Key available on request |
> -----Original Message-----
> From: Prem Raj [mailto:prbj_at_rediffmail.com]
> Sent: 19 September 2002 18:28
> To: amber_at_heimdal.compchem.ucsf.edu
> Subject: compiling without ISTAR2
>
>
> Dear Amber users,
> I started a dynamics simulation on a protein molecule
> with
> explicit water using Amber 6 ( sander_classic). The system has a
> total of
> 34800 atoms. when I ran the initail minimisation I got the below
> error.
> GROUP 8 HAS HARMONIC CONSTRAINTS 500.00000
> GRP 8 RES 141 TO 157
> Number of atoms in this group = 288
> ----- END OF GROUP READ -----
> Ligand Grid: OFF (not requested)
> Too many atoms for 16 bit pairlist -
> Recompile without ISTAR2
>
> In which file should I make these changes before I recompile the
> software.
>
> ************************************************************
> Prem Raj B. Joseph
> Dept. of Chemistry and Biochemistry
> Howard Hughes Medical Institute
> University of Maryland Baltimore County
> 1000 Hilltop Circle, Baltimore, MD 21250
> Ph: (410)455-2718
> email: prbj123_at_rediffmail.com
>
> Residence:
> 4747 Drayton Grn
> Baltimore, MD - 21227
> Ph(Res): (410)247-2413
> *************************************************************
>
>
> thanks in advance.
>
>
>
Received on Thu Sep 19 2002 - 10:50:49 PDT
