Re: Re: patch for phosphotyrosine residue

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Jun 22 2011 - 10:46:17 CDT

For your first issue you can use the pdbalias command to tell psfgen that
your P and O[1-3]P atom names should map to P1 and O[2-4] (or whatever
numbering makes sense for the oxygens).

For your second issue, par_all27_prot_na.prm is a parameter file. You
need to load top_all27_prot_na.rtf instead.

-Jim

On Wed, 22 Jun 2011, bharat gupta wrote:

> hi,
>
> Hi, I tried with patching of phosphotyrosine residue and this time the
> patch was done, but the phosphate ion structure has got distorted. I think
> it's due to the following errors that I got while doing patching:-
>
> coordpdb temp.pdb LIG
> reading coordinates from pdb file temp.pdb for segment LIG
> Warning: failed to set coordinate for atom O TYR:1 LIG
> Warning: failed to set coordinate for atom P TYR:1 LIG
> Warning: failed to set coordinate for atom O1P TYR:1 LIG
> Warning: failed to set coordinate for atom O2P TYR:1 LIG
> Warning: failed to set coordinate for atom O3P TYR:1 LIG
>> Main< (1-1-build) 46 % patch TP2 LIG:1
> applying patch TP2 to 1 residues
>> Main< (1-1-build) 47 % guesscoord
> Info: guessing coordinates for 16 atoms (6 non-hydrogen)
> Warning: poorly guessed coordinates for 9 atoms (6 non-hydrogen):
> Warning: poorly guessed coordinate for atom P1 TYR:1 LIG
> Warning: poorly guessed coordinate for atom O2 TYR:1 LIG
> Warning: poorly guessed coordinate for atom O3 TYR:1 LIG
> Warning: poorly guessed coordinate for atom O4 TYR:1 LIG
> Warning: poorly guessed coordinate for atom OT1 TYR:1 LIG
> Warning: poorly guessed coordinate for atom OT2 TYR:1 LIG
> Warning: poorly guessed coordinate for atom HT1 TYR:1 LIG
> Warning: poorly guessed coordinate for atom HT2 TYR:1 LIG
> Warning: poorly guessed coordinate for atom HT3 TYR:1 LIG
>
> What is the reason for this coordpdb command to fail. Also while executing
> the command topology topology par_all27_prot_na.prm, I got the following
> errors:-
>
> ERROR! FAILED TO RECOGNIZE ON6B
> ERROR! FAILED TO RECOGNIZE CN1
> ERROR! FAILED TO RECOGNIZE CN1A
> ERROR! FAILED TO RECOGNIZE CN1T
> ERROR! FAILED TO RECOGNIZE CN2
> ERROR! FAILED TO RECOGNIZE CN3
> ERROR! FAILED TO RECOGNIZE CN3A
> ERROR! FAILED TO RECOGNIZE CN3B
> ERROR! FAILED TO RECOGNIZE CN3C
> ERROR! FAILED TO RECOGNIZE CN3D
> ERROR! FAILED TO RECOGNIZE CN3T
> ERROR! FAILED TO RECOGNIZE CN4
> ERROR! FAILED TO RECOGNIZE CN5
> ERROR! FAILED TO RECOGNIZE CN5G
> ERROR! FAILED TO RECOGNIZE CN7
> ERROR! FAILED TO RECOGNIZE CN7B
> ERROR! FAILED TO RECOGNIZE CN7C
> ERROR! FAILED TO RECOGNIZE CN7D
> ERROR! FAILED TO RECOGNIZE CN8
> ERROR! FAILED TO RECOGNIZE CN8B
> ERROR! FAILED TO RECOGNIZE CN9
> ERROR! FAILED TO RECOGNIZE CNE1
> ERROR! FAILED TO RECOGNIZE CNE2
> ERROR! FAILED TO RECOGNIZE CNA
> ERROR! FAILED TO RECOGNIZE CNA2
> ERROR! FAILED TO RECOGNIZE CN6
> ERROR! FAILED TO RECOGNIZE CN7E
> ERROR! FAILED TO RECOGNIZE FN1
> ERROR! FAILED TO RECOGNIZE FNA
> ERROR! FAILED TO RECOGNIZE P
> ERROR! FAILED TO RECOGNIZE P2
> ERROR! FAILED TO RECOGNIZE P3
> ERROR! FAILED TO RECOGNIZE HBOND
>
> I tried to use auto angles dihedrals command , but there was no change in
> the phosphate ion part, it was still distorted...
>
> pls help ??
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010_at_yahoo.com
>

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