Re: patch for phosphotyrosine residue

From: bharat gupta (bharat.85.monu_at_gmail.com)
Date: Tue Jun 21 2011 - 20:53:38 CDT

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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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