VMD-L Mailing List

From: hodak_at_chips.ncsu.edu
Date: Mon Nov 21 2005 - 02:19:10 CST

Thanks for your help, but now I am getting NH and CO ends now.

My script is really simple.

        package require psfgen
        grep -v '^HETATM' his.pdb > protein.pdb
        grep 'HOH' his.pdb > water.pdb

        # Embed the psfgen commands in this script
        /opt/namd/psfgen << ENDMOL

        topology toppar/top_all22_prot.inp

        # His has to be specified as HSD, HSE or HSP
        pdbalias residue HIS HSE ;

        segment PROT {
          first NONE
          last NONE
          pdb protein.pdb
        }

        coordpdb protein.pdb PROT

        guesscoord
        writepsf out.psf
        writepdb out.pdb
        ENDMOL

        exit

his.pdb is dipeptide (containg H and G - no water) with neutral ends
created in pymol. I want psfgen to suggest better coordinates (that is why
I am using guesscoord) and to create psf and pdb files so that I can run
namd simulation. I also want to add solvent, but I want to get the ends
the way I want them. This is just a toy system to understand how vmd,
psfgen and namd work.

What am I doing wrong? Or, alternatively, is there a way to just add
solvent and generate psf file without altering original protein structure?

Thanks,
        Miro

Here is my his.pdb file:
ATOM 1 N HIS 2 0.498 -2.372 -1.127 1.00 0.00 N
ATOM 2 CA HIS 2 1.052 -1.053 -0.834 1.00 0.00 C
ATOM 3 C HIS 2 2.561 -1.080 -0.865 1.00 0.00 C
ATOM 4 O HIS 2 3.241 -0.072 -0.625 1.00 0.00 O
ATOM 5 CB HIS 2 0.551 -0.676 0.570 1.00 0.00 C
ATOM 6 CG HIS 2 -0.281 0.573 0.562 1.00 0.00 C
ATOM 7 CD2 HIS 2 -1.660 0.555 0.400 1.00 0.00 C
ATOM 8 ND1 HIS 2 0.197 1.873 0.711 1.00 0.00 N
ATOM 9 CE1 HIS 2 -0.959 2.556 0.620 1.00 0.00 C
ATOM 10 NE2 HIS 2 -2.108 1.850 0.438 1.00 0.00 N
ATOM 11 H HIS 2 1.129 -3.224 -1.332 1.00 0.00 H
ATOM 12 HA HIS 2 0.732 -0.370 -1.639 1.00 0.00 H
ATOM 13 2HB HIS 2 1.397 -0.517 1.268 1.00 0.00 H
ATOM 14 3HB HIS 2 -0.059 -1.483 1.027 1.00 0.00 H
ATOM 15 2HD HIS 2 -2.252 -0.346 0.268 1.00 0.00 H
ATOM 16 1HE HIS 2 -0.912 3.634 0.700 1.00 0.00 H
ATOM 17 2HE HIS 2 -3.075 2.194 0.348 1.00 0.00 H
ATOM 18 H01 HIS 2 -0.095 -2.257 -1.937 1.00 0.00 H
ATOM 19 N GLY 3 3.244 -2.340 -1.189 1.00 0.00 N
ATOM 20 CA GLY 3 4.675 -2.055 -1.141 1.00 0.00 C
ATOM 21 C GLY 3 5.402 -2.736 -2.274 1.00 0.00 C
ATOM 22 O GLY 3 4.811 -3.433 -3.105 1.00 0.00 O
ATOM 23 O01 GLY 3 6.818 -2.571 -2.391 1.00 0.00 O
ATOM 24 H GLY 3 2.767 -2.724 -2.079 1.00 0.00 H
ATOM 25 3HA GLY 3 5.051 -2.406 -0.225 0.00 0.00 H
ATOM 26 HA GLY 3 4.826 -0.964 -1.247 1.00 0.00 H
ATOM 27 H01 GLY 3 7.210 -2.546 -1.515 1.00 0.00 H
END

On Sun, 20 Nov 2005, Justin Gullingsrud wrote:

> Hi,
>
> Add the following 'first' and 'last' to your segment statements:
>
> segment A {
> first NONE
> last NONE
> pdb ....
> }
>
> Cheers,
> Justin
>
> On 11/18/05, hodak_at_chips.ncsu.edu <hodak_at_chips.ncsu.edu> wrote:
> > I am trying to create psf of a protein that has uncharged terminal ends
> > (i.e. NH2 and COOH instead of NH3+ and COO-), but psfgen always generates
> > charged ends.
> >
> > Is there any way to get psfgen to generate system with neutral terminal
> > ends?
> >
> > Help greatly appreciated.
> >
> > Miro
> >
>
>
> --
> Studying texts and stiff meditation can make you lose your Original Mind.
> A solitary tune by a fisherman, though, can be an invaluable treasure.
> Dusk rain on the river, the moon peeking in and out of the clouds;
> Elegant beyond words, he chants his songs night after night.
> -- Ikkyu, "The Fisherman"
>
>