Re: psfgen - ACE cap on PRO

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Mar 10 2011 - 19:59:14 CST

Hi Marc,
You need to use ACP instead of ACE for a C-terminal proline.
Best,
Peter

On 03/10/2011 08:07 PM, Marc Charendoff wrote:
> Hello,
>
> I have attempted to use the autopsf package to create a topology
> for an N-terminus ACE cap on a proline residue. The initial pdb looked a
> bit strange in VMD which I thought might be an artifact that would
> resolve after minimization. However, after 2000 steps of minimization, I
> still see a strange topology rendered for the ACE-PRO structure in VMD.
> I have listed my pdb and psf file portions below. My minimization was
> done using par_all27_prot_na.prm.
>
> Thanks, Marc
>
> PDB
>
>
> REMARK original generated coordinate pdb file
>
> ATOM 1 CAY ACE X 1 -15.305 1.914 0.532 1.00 0.00
> P1 C
>
> ATOM 2 HY1 ACE X 1 -15.847 1.726 -0.287 1.00 0.00
> P1 H
>
> ATOM 3 HY2 ACE X 1 -15.007 2.869 0.532 1.00 0.00
> P1 H
>
> ATOM 4 HY3 ACE X 1 -15.847 1.726 1.351 1.00 0.00
> P1 H
>
> ATOM 5 CY ACE X 1 -14.499 1.322 0.532 1.00 0.00
> P1 C
>
> ATOM 6 OY ACE X 1 -13.957 1.510 1.351 1.00 0.00
> P1 O
>
> ATOM 7 N PRO X 1 -14.517 0.748 -0.287 1.00 0.00
> P1 N
>
> ATOM 8 CD PRO X 1 -15.632 0.187 -1.322 1.00 0.00
> P1 C
>
> ATOM 9 HD1 PRO X 1 -16.083 -0.808 -1.100 1.00 0.00
> P1 H
>
> ATOM 10 HD2 PRO X 1 -16.454 0.937 -1.393 1.00 0.00
> P1 H
>
> ATOM 11 CA PRO X 1 -13.346 -0.113 -0.287 1.00 0.00
> P1 C
>
>
>
> PSF
>
>
> 8 !NTITLE
>
> REMARKS original generated structure x-plor psf file
>
> REMARKS 2 patches were applied to the molecule.
>
> REMARKS topology Peptide8_1_autopsf-temp.top
>
> REMARKS topology /Applications/VMD
> 1.8.6.app/Contents/vmd/plugins/noarch/tcl/solvate1.2/wat.top
>
> REMARKS segment P1 { first ACE; last CT2; auto angles dihedrals }
>
> REMARKS segment WT1 { first NONE; last NONE; auto none }
>
> REMARKS patch ACE P1:1
>
> REMARKS patch CT2 P1:8
>
>
> 9023 !NATOM
>
> 1 P1 1 ACE CAY CT3 -0.270000 12.0110 0
>
> 2 P1 1 ACE HY1 HA 0.090000 1.0080 0
>
> 3 P1 1 ACE HY2 HA 0.090000 1.0080 0
>
> 4 P1 1 ACE HY3 HA 0.090000 1.0080 0
>
> 5 P1 1 ACE CY C 0.510000 12.0110 0
>
> 6 P1 1 ACE OY O -0.510000 15.9990 0
>
> 7 P1 1 PRO N N -0.290000 14.0070 0
>
> 8 P1 1 PRO CD CP3 0.000000 12.0110 0
>
> 9 P1 1 PRO HD1 HA 0.090000 1.0080 0
>
> 10 P1 1 PRO HD2 HA 0.090000 1.0080 0
>
> 11 P1 1 PRO CA CP1 0.020000 12.0110 0
>
> 12 P1 1 PRO HA HB 0.090000 1.0080 0
>
>

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