Re: n terminal patch on proline

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Tue Aug 15 2006 - 12:53:37 CDT

hi all
      sorry for the previous incomplete mail. now i am adding my psfgen
script and the eroor message i got. here is the psfgen script.

package require psfgen

topology top_all27_prot_lipid.inp

topology fad_top.inp

pdbalias residue HIS HSE

pdbalias atom ILE CD1 CD

segment A {pdb chain_A.pdb}

coordpdb chain_A.pdb A

segment B {pdb chain_B.pdb}

coordpdb chain_B.pdb B

segment P {

patch PROPN P:2002

pdb pro.pdb

}

coordpdb pro.pdb P

segment F {pdb FAD.pdb}

coordpdb FAD.pdb F

guesscoord

writepdb prodh1.pdb

writepsf prodh1.psf

exit
and here is the error message i got.

building segment P

applying patch PROPN to 1 residues

ERROR: failed to apply patch

MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

ERROR: failed while building segment

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

can you please help me out from this problem.

On 8/15/06, Dhiraj Srivastava <dhirajks_at_gmail.com> wrote:
>
> hi all
> i am trying to apply n terminal patch on proline so that the N atom
> is not protonated and is neutral. this proline is not in polypeptide chain
> but is as a substrate of my enzyme. i have tried several times but i am not
> able to get a proline molecule with neutral amino group and a charged
> carboxylate group. how can i do that. proline binds to my protein in
> its -vely charged state and not in its zwiterionic form.
>
>
> --
> Dhiraj Kumar Srivastava
> Department of Chemistry
> University of Missouri-Columbia
> MO, 65211
> Ph. no. 001-573-639-0153
>

-- 
Dhiraj Kumar Srivastava
Department of Chemistry
University of Missouri-Columbia
MO, 65211
Ph. no. 001-573-639-0153

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