Mark,
Great email.
My vote it to do exactly what you suggest, being as consise as possible
without being vague.
Regards,
Mike
On 2/9/09 8:13 PM, "Mark Williamson" <mjw.sdsc.edu> wrote:
> Dear all,
>
> I am currently helping with the implementation of the CHARMM forcefield
> within AMBER along with Mike Crowley and Ross Walker. It is getting
> there, and I am currently working on CMAP energies and gradients.
>
> Here is a sample of what chamber (the tool for converting CHARMM psf and
> parameter files to AMBER) is outputting at the moment to a CHARMM
> enabled prmtop file:
>
>
> %FLAG CHARMM_CMAP_COUNT
> %COMMENT Number of CMAP terms, number of unique CMAP parameters
> %FORMAT(2I8)
> 157 4
> %FLAG CHARMM_CMAP_RESOLUTION
> %COMMENT Number of steps along each phi/psi CMAP axis
> %COMMENT for each CMAP parameter
> %FORMAT(20I4)
> 24 24 24 24
> %FLAG CHARMM_CMAP_PARAMETER_01
> %COMMENT C NH1 CT1 C NH1 CT1 C NH1
> %FORMAT(8(F9.6))
> 0.126790 0.768700 0.971260 1.250970 2.121010 2.695430 2.064440 1.764790
> 0.755870-0.713470 0.976130-2.475520-5.455650-5.096450-5.305850-3.975630
> -3.088580-2.784200-2.677120-2.646060-2.335350-2.010440-1.608040-0.482250
> ...snip...
> %FLAG CHARMM_CMAP_PARAMETER_02
> %COMMENT C NH1 CT2 C NH1 CT2 C NH1
> %FORMAT(8(F9.6))
> -0.549160-0.535500-0.588110-0.754620-0.679290-0.038150 0.298460 0.326040
> -0.375610-1.704360-3.061280-3.956460-3.576280-1.038930 2.012450-1.714610
> -0.377660 0.317310 0.294580-0.042920-0.676620-0.744600-0.586590-0.554770
> ...snip.....
> %FLAG CHARMM_CMAP_INDEX
> %COMMENT Atom index i,j,k,l,m of the cross term
> %COMMENT and then pointer to CHARMM_CMAP_PARAMETER_n
> %FORMAT(6I8)
> 18 20 22 37 39 1
> 37 39 41 48 50 1
> 48 50 52 67 69 1
> ...snip....
>
> Having looked through the nxtsec.f code, I have some general question
> about comments in prmtop files:
>
> a) Does anyone mind me being verbose in a following %COMMENT line(s) to
> %FLAG as to what the %FLAG is describing?
>
> b) Can a %COMMENT line follow a previous one? (I personally would like
> to take around four lines to explain exactly what is going on and
> perhaps even go some way to help to remove the need for the
> http://ambermd.org/formats.html#topology file ;) )
>
> c) Is having a specific flag for each CMAP term (%FLAG
> CHARMM_CMAP_PARAMETER_n) a good strategy? Looking through the amoeba
> code, that Tom Darden used an approach like this.
>
> d) Any general pointers and/or hints+tips on the right thing to do here,
> and what to avoid?
>
> Thanks,
>
> Mark
>
>
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Received on Wed Feb 11 2009 - 01:19:45 PST
