From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Jan 23 2013 - 11:16:32 CST
I have no idea what you're trying to do here, but it looks very non-standard. Try using the Mutator plugin in VMD on your original structure (with the FEP box checked) to produce the files you need.
On Jan 23, 2013, at 12:07 PM, Thomas Albers wrote:
> Hello!
>
>> Explain in precise detail how you built the PSF. Likely you are missing some needed terms.
>
> I put together one example like so:
>
> --snip--
> resetpsf
> topology top_all27_prot_lipid.rtf
> segment M {
> first NTER
> last CTER
> residue 605 ALA
> }
>
> coord M 605 C { 13.555 10.868 -0.780 }
> coord M 605 N { 13.092 9.947 1.685 }
> coord M 605 CA { 13.798 9.880 0.329 }
> guesscoord
>
> readpsf I119A.psf
> coordpdb I119A-2.pdb
>
> writepsf TEST-ALA.psf
> writepdb TEST-ALA.pdb
> --snap--
>
> On my laptop with the NAMD-2.9-Linux-x86_64-multicore binary this
> gives the expected results, but on our cluster with a NAMD-2.9 that we
> compiled ourselves the trajectories look *very* odd. Something is
> wrong with NAMD, at least with our installation.
>
> Thomas
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