Belly option in sander

From: Florian Barth <>
Date: Wed 31 Jan 2001 19:17:51 +0100

Dear Amber users,

I would like to run a md simulation in sander using the belly option to constrain the protein backbone. This is my

#50ps simulated annealing with temp. ramp and Belly
      nstlim=25000, dt=0.002, ntt=1, ibelly=1, igb=3, ntb=0, cut=12.0, ntpr=100, ntwr=500, ntwx=50,
#temp. ramp
      type='TEMP0', istep1=0, istep2=1000, value1=0.0, value2=150.0,
      type='TEMP0', istep1=1001, istep2=5000, value1=150.0, value2=300.0,
      type='TEMP0', istep1=5001, istep2=25000, value1=300.0, value2=300.0,
#temp. coupling
      type='TAUTP', istep1=0, istep2=5000, value1=0.2, value2=0.2,
      type='TAUTP', istep1=5001, istep2=10000, value1=0.2, value2=2.0,
      type='TAUTP', istep1=10001, istep2=25000, value1=2.0, value2=2.0,
 #constrain backbone
* * S *
* * B *
* * 3 *
* * E *
RES 1 455
RES 456 501

The first problem with sander is, that it apparently only accepts the GROUP input right after the &cntrl namelist containing the IBELLY flag. Therefore, with above file
sander interprets the &wt namelist as GROUP input.
After deletion of all namelists except the &cntrl one, sander breaks up with the remark:
"When igb>0, the moving part must be at the start of the molecule. This does not seem to be the case here."

Does anybody know, how the or the topology files must be altered to run above simulation in sander. A colleague pointed out to me, that it is possible with
sander_classic to run belly simulations but I would like to stick to the "new" sander.
Thanks a lot in advance

Florian Barth

Institute of Technical Biochemistry
University of Stuttgart
Allmandring 31
70569 Stuttgart
Received on Wed Jan 31 2001 - 10:17:51 PST
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