Re: n terminal patch on proline

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Aug 15 2006 - 14:04:59 CDT

Dear Dhiraj,
could you let us know where you got your patch from? You have a "PROPN"
patch listed in your file, but the only proline N-terminal patch in the
standard charmm topology files is PROP, which is a protonated version.
Best,
Peter

Dhiraj Srivastava wrote:
> 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
> <mailto: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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