Try putting "GROUP" and the name you assign it on thte same line, i.e.
"GROUP Mg" and "GROUP Protein" in your example below.
Best,
Natasja
Natasja Brooijmans
Graduate Program in Chemistry & Chemical Biology
Department of Pharmaceutical Chemistry
University of California, San Francisco
San Francisco, CA 94143-0446
phone: 415-476 8291
fax: 415-502 1411
e-mail: nbrooij_at_itsa.ucsf.edu
On Fri, 6 Dec 2002, Numan Oezguen wrote:
> Dear all,
>
> First I would to thank David Case for the response/hint about the GROUP keyword.
> Unfortunately removing this keyword from the anal.in file didn't change the
> output at all. Is there anyone who have used ANAL to do energy decomposition, or
> is it only a non working relict taken over from earlier AMBER version? By the
> way I am still using AMBER6. How can I get the different energy contribution for
> a given snapshot of the MD-runs?
>
> Here again my original question:
> I am doing MD-Simulation on a system with a protein, DNA, Mg2+ and water.
> Dependent on the initial position of Mg2+ it's moving during the simulation. I
> want to know what are the driving forces, what are the energy contributions of
> the surrounding residues. To my understanding the ANAL program should be used
> for such analysis. As parameter file I use the *.top file generated with XLEAP
> and the coordinate input file is the last restart file of the MD run.
>
> Appreciate any help/comment
>
> Numan
>
> I execute this command:
> =================================================================
> anal -O -i anal.in -o anal.out -p md16.top -c md16.rst
> =================================================================
>
> Here is my anal.in:
> =================================================================
> Magnesium interactions
> 1 0 0 0 70 1
> 2 62.6413970 79.2115252 58.4662127 0
> 1 0 2 1 9999 1
> 999.0 2.0 1.2 1.0
> 1 -1.0E40 -1.0E40 -1.0E40 -1.0E40 -1.0E40 -1.0E40 -1.0E40 -1.0E40 -1.0E40
> ENERGY
> GROUP
> Mg
> RES 299
> END
> Protein
> RES 1 298
> END
> END
> STOP
> =================================================================
>
> And here is the output anal.out:
> =================================================================
> ---------------------------------------------------------------
> Amber 5.0 ANAL: Static Analysis for Energy/Structure UCSF 1997
> ---------------------------------------------------------------
>
>
>
> 1. RESOURCE USE:
>
>
> Memory Use Allocated Used
> Real 5000000 597834
> Integer 5000000 500933 (static)
>
> | Max Nonbonded Pairs: 8998134 packed 2 to a machine word
>
>
> 2. DATA CONTROL:
>
> Magnesium
> interactions
>
> NTX = 1 NTXO = 0 NRC = 0
> NRCX = 0 NGRPX = 70 KFORM = 1
>
> NTB = 2 BOXX = 62.641 BOXY = 79.212
> BOXZ = 58.466 BETA = 0.000
>
> NTF = 1 NTID = 0 NTN = 2
> NTNB = 1 NSNB = 9999 IDIEL = 1
>
> RCUT = 999.00 SCNB = 2.00
> SCEE = 1.20 DIELC = 1.00
>
> IMAX EBMAX EANMAX EDIHMAX ENB14MAX
> 1 -inf -inf -inf -inf
>
> EEL14MAX ENBMAX EELMAX EHBMAX ECONSMAX
> -inf -inf -inf -inf -inf
>
>
> 3. A T O M I C C O O R D I N A T E S
>
>
>
>
> NUMBER OF ATOMS = 30413
>
>
> End of Input File Reached
> =================================================================
>
>
Received on Fri Dec 06 2002 - 09:24:21 PST
