Minimization using Fixed Atoms

From: Rita Cassia (
Date: Fri Aug 10 2007 - 05:16:48 CDT

Dear NAMD users,

for me its the first time that Im doing minimization , using this option. I have a chromophore complex, solvated in a methanol box. I have produced the topology and input coordinates, also the library and pdb files with amber (xleap).
Okay, then I opened vmd, in order to write a new pdb file, that would have the information, which atoms should be kept fixed, during the first minimization.
What I did, in tcl window, was:
"set all [atomselect top all],
set fix [atomselect top "resid 1 to 21"] : this means that only the chromophore structure should be fixed and the methanol molecules should be free
$all set beta o
$fix set beta 1
$all writepdb P16_fixed_resid.pdb"

Then, in the conf. file, I wrote a flag, to indicate that the chromophore complex should be fixed :

# Fixed Atoms Constraint (set PDB beta-column to 1)
# -----------------------------------------------------------
if {1} {
fixedAtoms on
fixedAtomsFile P16_fixed_resid.pdb
fixedAtomsCol B

And as input files: the topology and the input coordinates, produced with amber : P16meoh.prmtop, P16meoh.inpcrd.

The minimization does not work:
the first error message was: Charm++ fatal error:
FATAL ERROR: Number of atoms in fixed atoms PDB doesn't match coordinate PDB

then I changed the initial coordinate file from P16meoh.inpcrd to P16meoh.pdb (pdb produced in leap, one that was used in vmd, to produced P16_fixed_resid.pdb).
Error message: Charm++ fatal error:
FATAL ERROR: Num of atoms in coordinate file is different from that in parm file!

I would be very greatful if someone could help me.

Thanks in advance


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