Re: Minimization using Fixed Atoms

From: Peter Freddolino (
Date: Fri Aug 10 2007 - 10:25:01 CDT

Hi Rita,
I'm sorry to ask a silly question, but have you inspected the pdb files
to ensure that they have the expected number of atoms (and that
visually, they match the param file)?
Also, I noticed that you're setting the beta field of some of your atoms
to "o" (the letter), rather than "0" (the number). This may cause
problems, as the beta field should contain a floating point number.


Rita Cassia wrote:
> 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
> Rita

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