AMBER Archive (2004)

Subject: Re: AMBER: idecomp

From: Marcela Madrid (
Date: Thu Jul 08 2004 - 14:35:57 CDT

I am trying to decompose the energy between residues by using sander 7
with idecomp and igb >0.

First of all, David, thanks for your answer. Your suggestion worked and
I got past the first problem by using igb =1.

I could not find in the manual or examples how to specify the residues
between which I want the energies when using idecomp. I tried the
following in order to obtain the wan der waals interaction between
residues 1 and 2:

  idecomp = 3
Group 1
Group 2

But this gives the following error message:
  Atom 989 ( 96 ) : 96, 1
  Atom 990 ( 96 ) : 96, 1
  Too many pairwise contributions for
    energy decomp requested.
    => 9216 .GT. 96

The manual says to use RRES and LRES with idecomp, but I could not find
these names. I found RECRES and LIGRES in the mm_pbsa section and
assumed this is what was meant. However I got the same error message. I
would appreciate any help on this, thank you very much, Marcela

David A. Case wrote:
> On Tue, Jul 06, 2004, Marcela Madrid wrote:
>>I am trying to find the value of the van der waals interactions between
>>two residues. I thought I could use IDECOMP to do this, using my sander
>>input file that does MD. I am using sander 7. The manual says that
>>IDECOMP is incompatible with ewald. So I tried to turn ewald off by
>>using in vacuum inpcrd and prmtop files, and setting ntb =0.
>>I am getting an error message that use_pme is unkown. If I delete
>>"use_pme=0" then I get an error message saying that idecomp is
>>incompatibe with ewald.
> I think IDECOMP is only available with GB calculations; so try setting igb>0.
> This should give you what you want (you can ignore the GB stuff if you are
> just interested in van der Waals interactions.)
> ...dave
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