AMBER Archive (2003)

Subject: RE: inter & intra-molecular interaction energies

From: Xiang, Tian-Xiang (txian2_at_email.uky.edu)
Date: Thu Feb 13 2003 - 17:47:54 CST

My amber6 does not have the directory $AMBERHOME/test/vac_rna. I tried
to run Anal program anyway. The run stopped very soon with the output
results file (analout) looks like the following at the end of the file:

" 2. DATA CONTROL:
  anal input file
     NTX = 1 NTXO = 0 NRC = 0
     NRCX = 0 NGRPX = 70 KFORM = 1
     NTB = 1 BOXX = 56.100 BOXY = 54.900
     BOXZ = 57.500 BETA = 90.000
     NTF = 1 NTID = 1 NTN = 1
     NTNB = 1 NSNB = 1 IDIEL = 1
     RCUT = 12.00 SCNB = 2.00
     SCEE = 1.20 DIELC = 1.00
     IMAX EBMAX EANMAX EDIHMAX ENB14MAX
         1 -100.00 -10.00 -10.00 -100.00
     EEL14MAX ENBMAX EELMAX EHBMAX ECONSMAX
         0.00 0.00 0.00 0.00 0.00

 3. A T O M I C C O O R D I N A T E S

          NUMBER OF ATOMS = 2298"

Apparently, the program got all the input parameters right, but it
stopped at getting the coordinates (my inpcrd and prmtop files were
generated using saveamberparm in xLeap, so they should not be wrong). I
tried several times without success using other inpcrd and prmtop files.
My input file is listed here:
---------------------------------------------------
   anal input file
   1 0 0 0 0 1
   1 56.1000000 54.9000000 57.5000000 90.0000000
   1 1 1 1 1 1
   12.0 2.0 1.2 1.0
   1 -100.0 -10.0 -10.0 -100.0 0.0 0.0 0.0 0.0 0.0
   ENERGY
Group 1
RES 1
END
Group 2
RES 2
END
END
STOP
---------------------------------------------------

Something wrong with this input file? Your help is greatly appreciated.
I also wonder if you could send me a generic input file since I don't
have one.

Tian-xiang

-----Original Message-----
From: David A. Case [mailto:case_at_scripps.edu]
Sent: Thursday, February 13, 2003 6:21 PM
To: Tian-Xiang Xiang
Cc: amber_at_heimdal.compchem.ucsf.edu
Subject: Re: inter & intra-molecular interaction energies

On Thu, Feb 13, 2003, Tian-Xiang Xiang wrote:
>
> I have simulated a peptide in a box of solvent molecules using Sander.
I
> need to know the intra-molecular Interaction of the peptide and the
> inter-molecular interaction of the peptide with surrounding solvents.
What
> is the best program to do this? The only program I know that might be
able
> to do this is
>
> ???Anal???, but I don???t have an example input file that I can modify
to my
> need. The manual is pretty hard to follow.
>

There are sample anal input files in $AMBERHOME/test/vac_rna. Maybe
those
will help. Don't be afraid to do some trial and error.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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