AMBER Archive (2002)

Subject: Sander segmentation fault

From: Joel Konkle-Parker (joelkp_at_ERC.MsState.Edu)
Date: Thu Oct 17 2002 - 14:28:48 CDT

I'm getting a "segmentation fault" when I run the following command:

----------------
sander -O -i md.belly.in -o md.belly.out -p polyAT.prmtop -c
min.belly.restart -r md.belly.restart -x md.belly.traj &
----------------

The input file is:

----------
5DNB, initial dynamics w/ belly on DNA, model1, 9.0 cut
  &cntrl

   ntpr = 10, ntwx = 500,

   ntf = 2, ntb = 2,
   cut = 9.0,

   ibelly = 1,

   nstlim = 12500,
   nscm = 0,
   dt = 0.002,

   temp0 = 300.0, tempi = 100.0,
   ntt = 1,
   tautp = 0.2,

   ntp = 1,

   ntc = 2, tol = 0.0005,

  &end
  &wt
    type='TEMP0', istep1=0, istep2=500,
                  value1=100.0, value2=300.0,
  &end
  &wt
    type='TEMP0', istep1=500, istep2=12500,
                  value1=300.0, value2=300.0,
  &end
  &wt
    type='END',
  &end
  &rst
    iat=0,
  &end
Allowing only the water and counterions to move in the belly
RES 21 3547
END
END
----------

and the output file (before it crashes, anyway) is (note the excess
spaces at the end):

----------

           -------------------------------------------------------
           Amber 7 SANDER Scripps/UCSF 2002
           -------------------------------------------------------

| Thu Oct 17 14:18:51 2002

   [-O]verwriting output

File Assignments:
| MDIN: md.belly.in

| MDOUT: md.belly.out

|INPCRD: min.belly.restart

| PARM: polyAT.prmtop

|RESTRT: md.belly.restart

| REFC: refc

| MDVEL: mdvel

| MDEN: mden

| MDCRD: md.belly.traj

|MDINFO: mdinfo

|INPDIP: inpdip

|RSTDIP: rstdip

  Here is the input file:

5DNB, initial dynamics w/ belly on DNA, model1, 9.0 cut

  &cntrl

 

   ntpr = 10, ntwx = 500,

 

   ntf = 2, ntb = 2,

   cut = 9.0,

 

   ibelly = 1,

 

   nstlim = 12500,

   nscm = 0,

   dt = 0.002,

 

   temp0 = 300.0, tempi = 100.0,

   ntt = 1,

   tautp = 0.2,

 

   ntp = 1,

 

   ntc = 2, tol = 0.0005,

 

  &end

  &wt

    type='TEMP0', istep1=0, istep2=500,

                  value1=100.0, value2=300.0,

  &end

  &wt

    type='TEMP0', istep1=500, istep2=12500,

                  value1=300.0, value2=300.0,

  &end

  &wt

    type='END',

  &end

  &rst

    iat=0,
----------

Can anyone see what's causing this?

- Joel