From: Andrea Diaz (andreadiaz2007_at_gmail.com)
Date: Sun Feb 03 2008 - 16:29:59 CST
I am trying to run a minimization of a protein system + water. I have run
the same system before in the same conditions but just with different sizes
and I did not have any problem with the simulation. I have run the protein
system using the same parameter file always without problem. Then I added
two boxes of water to the cylindrical peptide system and I have used psfgen
to create the water psf files of the water. After this I have used a merge
tcl script to put all the .pdb and .psf files together. I have done this
exact procedure with the same protein but smaller diameter and it did not
have any problem.
The minimization is not runing because of this error:
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE HN.
The atom HN is present in the ALA and GLN amino acids of the system, and
both of them are included in the parameter file.
I have find this problem in some way different from the one previously
posted in the list, about the CN7 atom, as the ALA is a common aminoacid
already included in the parameter file that I have. Also I am wondering why
the protein without water runs OK and after merging the independents
structures the problems came out.
>From the wikyNAMDandCharmm web information I have also found that you don't
specify a segment name, the second column in the psf file will be blank and
NAMD will misread the charge as the atom type; but I don't see this as my
case, because my .psf contains the segment name of all the atoms.
My merge.tcl file looks like :
mol load psf solvpept10_3.psf pdb solvpept10_3.pdb
I really appreciate any help, I have been trying to solve the problem in
different ways but any thing I have tried had worked fine.
Texas A&M University
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