Re: Interface program installation

From: David Pearlman <>
Date: Fri 19 Oct 2001 16:22:45 -0500


It appears that someone made some modifications to the Interface
install stuff when version 6 was sent out, but the mods were not
fully/correctly updated...

To install Interface:

1) Go to the src/interface/source directory and issue the
   command "Make" to compile the Interface program

2) Go to the src/interface/etc directory and issue the command
   "Make" to compile the Interface accessory programs.

3) It appears that versions of the Amber6 distribution are going out
   with a "null" amber.def file in the Interface "def" directory. I do
   not know how this happened; it was certainly NOT null when I created
   it! At any rate, below you will find an
   attachment which is the amber.def file that should have been included.

   A) Place the attached Amber.def file in src/interface/def
   B) Go to directory /src/interface
   C) source install_ambint

And you should be done.


Sophia Kondratova wrote:
> Hello,
> I have tried to install the Interface program and I have followed the
> instructions for the script install_ambint, which makes an amber.dat file in
> the /tmp dir, but when I open this file, it does not contain any commands at
> all. As well the amberint manual talked about what was suppose to be in the
> amber.def file (the commands in there), and when I opened the amber.def file
> in the amber6 dir, it was also blank. I am not sure if the install_int script
> did not install Interface properly, but when I type
> /usr/local/amber6/exe/interface -t
> /usr/local/amber6/src/interface/tmp/amber.dat -i testgibb.example the
> following error is shown
> -ERROR - from routine: RDUCOM
> Unrecognized command in user_command_file: gibbs
> Current UC-file line (from testgibb.example):
> gibbs
> Last TEMPLATE-file line (from ):
> (none)
> I think that there is something wrong with the amber.def file, because as I
> undersand it, its suppose to contain commands that will make up the amber.dat
> file
> Any help would be greatly appreciated.
> Sophia Kondratova
> Biochemistry Graduate Student
> University of New Brunswick
> Fredericton, Canada! This is the IPS script for the AMBER MINMD/SANDER/GIBBS interface
! Author: David A. Pearlman
! Date: 2/91 -ff

!**************************** COPYRIGHT NOTICE ********************************
! This software is Copyright (c) 1991 David A. Pearlman, All Rights Reserved **
! This software is provided under license and may not be used, copied, **
! modified, transmitted, inspected or executed by any means whatsover **
! without the express written consent of the Copyright holder. **
!**************************** COPYRIGHT NOTICE ********************************

  echo " AMBER/Interface front-end template (v 5.0) read"

! Define the directory path containing the needed files. Replace the string
! between quotes with the complete directory specification of location of
! the IPS scripts on your machine. Note that all punctuation to preceed the
! filename must be given here. Thus, we include the trailing / for a unix
! directory:

 REDIRECT = "/vrtx/work1/dap/def/amber60/" /DEFAULT

! assign the names of the programs to be run (if RUN specified)
! In each case, provide the complete program specification. Replace the
! strings between the quotes:

  ASSIGN PROGRAM_USE_MINMD = "/vrtx/work1/dap/amber4/exe/minmd"
  ASSIGN PROGRAM_USE_SANDER = "/vrtx/work1/dap/amber4/exe/sander_new"
  ASSIGN PROGRAM_USE_GIBBS = "/vrtx/work1/dap/amber4/exe/gibbs4"
  ASSIGN PROGRAM_USE_PDBGEN = "/vrtx/work1/dap/amber4/exe/pdbgen"

! Assign the name of the dirctory to contain all the utility programs. Include
! any required trailing punction as for the REDIRECT command above. Replace
! the string between the quotes:

  ASSIGN UTILITY_DIR = "/vrtx/work1/dap/amber/bin/"

! **** Done with machine-dependent specifications *****.

! Initialize all variables to -99989. Just a safety precaution.
 DEFINE RNOF = -99989.0

 nvassign info = 0
 nvassign ilogcom = 0
 nvassign ispecial_out = 0
 nvassign ap_str = " "
 nvassign ivms = 0
 define prompt = "ambint\> "
 define ifocnt = 2

! set initial memory mark:


! Echo all messages with an indent of 5:
 echo end=79/indent=5/default

! ***************************************************************************
! Read the DEFER block which sets unitialized variables and does the actual
! variable writes. defer.def itself picks the appropriates writes depending
! on the type of run (includes additional REDIRECTS).

  REDIRECT = "defdir:defer.def"

! ***************************************************************************
! Read the definitions of commands common to MINMD & GIBBS from both.def:

  REDIRECT = "defdir:both.def"

! ***************************************************************************
! Read the definitions of commands only interpreted in GIBBS (skipped in
! MINMD /SANDER) from gibbsonly.def

  REDIRECT = "defdir:gibbsonly.def"

! ***************************************************************************
! Get the TEMP command definition from temp.def

  REDIRECT = "defdir:temp.def"
! ***************************************************************************
! Read the definitions of commands only interpreted in MINMD/SANDER (skipped in
! GIBBS) from minmdonly.def

  REDIRECT = "defdir:minmdonly.def"

! ***************************************************************************
! Read the definitions of the GROUP command

  REDIRECT = "defdir:group.def"

! ***************************************************************************
! Read the definitions specific to NMR-type restraints from nmr.def
! These commands are recognized but ignored in MINMD and GIBBS (only used
! in SANDER).

  REDIRECT = "defdir:nmr.def"

! ***************************************************************************
! Read the definition of the Ewald command. This has been updated to
! be usable with V6.0 Sander_PME

  REDIRECT = "defdir:ewald.def"

! ***************************************************************************
! Read the definition of the CNST (constraint definition) command:
! This command only has an effect in GIBBS.

  REDIRECT = "defdir:cnst.def"

! ***************************************************************************
! Read the definitions of the RUN command.

  REDIRECT = "defdir:run.def"

! ***************************************************************************
! Read the common utility command definitions from file misc.def

  REDIRECT = "defdir:misc.def"

! Read any other definitions:

  REDIRECT = "defdir:timavg.def"
Received on Fri Oct 19 2001 - 14:22:45 PDT
Custom Search