VMD-L Mailing List

From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Mon Nov 21 2005 - 11:49:19 CST

Hi,

You probably want an acetylated N terminus, then, which you can get by
specifying "first ACE". I'm not sure what kind of C terminus you're
looking for, but check out the PRES patches in the topology file to
see what's available.

Hope this helps,
Justin

On 11/21/05, hodak_at_chips.ncsu.edu <hodak_at_chips.ncsu.edu> wrote:
> 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"
> >
> >
> 

--
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"