AMBER Archive (2003)

Subject: using distance restraints in Sander (AIX 4.3 RS6000)

From: Wayne Dawson (dawson_at_nih.go.jp)
Date: Fri May 16 2003 - 03:33:02 CDT

Dear User list,

This seems like it should be a simple problem, but I
just cannot seem to get a simple distance restraint
to work in Amber7. I know for the example below, I
can use the "bond" command in xleap, but my purpose
is to learn how to use Amber and this is an easy
example.

I'm using an IBM RS6000 (AIX v.4.3).

I also cannot understand why I keep getting these
NAMELIST errors. Again, I've tried all sorts of formats,
copied things from the manual and the website, changed
parameters etc., used "#" but I always seem to get this
same error message. If I remove the "END" in the file below,
I get only one of them. The program does work fine if
nmropt=0, but it still gives the error message. I thought
you were supposed to be able to add comments in these files.

Here's the output.

dawson% sander -O -i md1z.in -o proteinBox.out -p proteinBox.crd -ref RST
1525-090 The NAMELIST READ statement cannot be completed because an incorrect character was encountered in a NAMELIST group name or item name. The program will recover by discontinuing further processing of the READ statement.
1525-090 The NAMELIST READ statement cannot be completed because an incorrect character was encountered in a NAMELIST group name or item name. The program will recover by discontinuing further processing of the READ statement.
1525-001 The READ statement on the file fort.9 cannot be completed because the end of the file was reached. The program will stop.
dawson%

And here is a summary of the relevant files where I'm
making a weak disulfide bond.

dawson% cat proteinBox.pdb | grep SG
ATOM 98 SG CYS 7 28.570 8.839 30.283
ATOM 256 SG CYS 18 29.801 14.754 25.259
ATOM 327 SG CYS 23 36.031 17.082 24.032
ATOM 615 SG CYS 42 25.714 19.994 18.943

dawson% cat RST
#
# 18 CYS SG 23 CYS SG 2.8 3.2
&rst
  ixpk= 0, nxpk= 0, iat= 256, 327, r1= 2.30, r2= 2.80, r3= 3.20, r4= 3.70,
      rk2=2.0, rk3=2.0, ir6=1, ialtd=0,
&end
&rst
  iat = 0,0,0,0,
&end

dawson% cat md1z.in
MD simulation, 50 ps
&cntrl
   nstlim=50000,
   nmropt=1,
   ntwr = 100,
   ntpr=200,
   ntt=1,
   ntwx=200,
   cut=15.0,
   ntb=0,
   vlimit=10,
   tempi = 300.0,
   temp0 = 300.0,
   tautp = 1.0,
&end
&ewald
   eedmeth=5,
&end
END