Re: Parameter File

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sun Jan 31 2010 - 21:34:21 CST

The one is the alanine demo is limited in scope, and possibly even outdated. The best place to go to is the source of the CHARMM forcefield: http://mackerell.umaryland.edu/CHARMM_ff_params.html

There, you will also find the topology files needed to include DNA in your PSF file, if you decide you want to later.

It's probably best if you go through the NAMD tutorial too.

On Jan 31, 2010, at 9:19 PM, Scooter Willis wrote:

>
> 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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