Parameter File

From: Scooter Willis (HWillis_at_scripps.edu)
Date: Sun Jan 31 2010 - 21:19:32 CST

Getting started with VMD and NAMD to explore Interactive Molecular Dynamics of a protein structure we are working with in the lab. 3DZY

I went through the the tutorial and was able to get the alanin demo working. Simple enough!

I then went down the path of using VMD to create a psf file using the automatic PSF builder. Ran into a series of errors related to DNA and ligands so I deleted them out of the original PDB structure and reran.

Very little is mentioned regarding the parameter file so I am using the one that came with alanin demo and I have now reached the extent of what is happening under the covers.

When I load into NAMD2(Running 2.7b2) I get the following error FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CT1. It also looks like I have other atom types that are probably not defined but haven't got past the first one yet. See PSF file example below.

I did a quick google search and see this type of problem is common but couldn't really find how to solve it.

My first question is Should I be using the parameter file from the alanin demo?

If not, I couldn't find anything in the tutorial that take someone through the process hoping that is straight forward.

By deleting the DNA and Ligands from the original PDB structure not sure if I need to clean anything up. I actually want to explore the dynamics of the protein without DNA or Ligand in a very simple way.

Any guidance on what I am missing as a basic concept would be greatly appreciated. I am new to molecular modeling so still working my way through the learning curve.

Thanks

Scooter Willis

Example PSF

   10583 !NATOM
       1 P1 132 LYS N NH3 -0.300000 14.0070 0
       2 P1 132 LYS HT1 HC 0.330000 1.0080 0
       3 P1 132 LYS HT2 HC 0.330000 1.0080 0
       4 P1 132 LYS HT3 HC 0.330000 1.0080 0
       5 P1 132 LYS CA CT1 0.210000 12.0110 0
       6 P1 132 LYS HA HB 0.100000 1.0080 0
       7 P1 132 LYS CB CT2 -0.180000 12.0110 0
       8 P1 132 LYS HB1 HA 0.090000 1.0080 0
       9 P1 132 LYS HB2 HA 0.090000 1.0080 0
      10 P1 132 LYS CG CT2 -0.180000 12.0110 0
      11 P1 132 LYS HG1 HA 0.090000 1.0080 0
      12 P1 132 LYS HG2 HA 0.090000 1.0080 0
      13 P1 132 LYS CD CT2 -0.180000 12.0110 0
      14 P1 132 LYS HD1 HA 0.090000 1.0080 0
      15 P1 132 LYS HD2 HA 0.090000 1.0080 0
      16 P1 132 LYS CE CT2 0.210000 12.0110 0
      17 P1 132 LYS HE1 HA 0.050000 1.0080 0
      18 P1 132 LYS HE2 HA 0.050000 1.0080 0
      19 P1 132 LYS NZ NH3 -0.300000 14.0070 0
      20 P1 132 LYS HZ1 HC 0.330000 1.0080 0
      21 P1 132 LYS HZ2 HC 0.330000 1.0080 0
      22 P1 132 LYS HZ3 HC 0.330000 1.0080 0
      23 P1 132 LYS C C 0.510000 12.0110 0
      24 P1 132 LYS O O -0.510000 15.9990 0
      25 P1 133 HSD N NH1 -0.470000 14.0070 0
      26 P1 133 HSD HN H 0.310000 1.0080 0
      27 P1 133 HSD CA CT1 0.070000 12.0110 0
      28 P1 133 HSD HA HB 0.090000 1.0080 0
      29 P1 133 HSD CB CT2 -0.090000 12.0110 0
      30 P1 133 HSD HB1 HA 0.090000 1.0080 0
      31 P1 133 HSD HB2 HA 0.090000 1.0080 0
      32 P1 133 HSD ND1 NR1 -0.360000 14.0070 0
      33 P1 133 HSD HD1 H 0.320000 1.0080 0
      34 P1 133 HSD CG CPH1 -0.050000 12.0110 0
      35 P1 133 HSD CE1 CPH2 0.250000 12.0110 0
      36 P1 133 HSD HE1 HR1 0.130000 1.0080 0
      37 P1 133 HSD NE2 NR2 -0.700000 14.0070 0
      38 P1 133 HSD CD2 CPH1 0.220000 12.0110 0
      39 P1 133 HSD HD2 HR3 0.100000 1.0080 0

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