From: Hidekazu WATANABE (evergreen_tow_at_yahoo.co.jp)
Date: Fri Jul 15 2005 - 05:19:19 CDT
Dear all
Thank you for kind response when I previously asked about the fixed
atoms.
Now, I try to patch the residue with topology file,
but the modifications of some of them are always failed.
The sample shown in the last is the gramicidin dimer which I'm trying
to calculate.
It consists of two same amino-chains, and both chains begin with VAL
(VAL:1 and VAL:18).
The N-terminations of these two VALs are wanted to be modified by
formyl group HCO-,
(patch FOR), consisting of the atoms HAY, CY, and OY.
The modification with patch FOR is correctly carried out for VAL:18,
but extra hydrogen atoms, HT1, HT2, and HT3 are added for VAL:1,
though VAL:1 and VAL:18 have completely same atomic conformation.
The extra hydrogen atoms, HT1, HT2, and HT3 are used in the regular
N-termination,
and then, VAL:1 is modified with not only "patch FOR", but also regular
N-terminated patch.
Is this because the VAL:1 is written in the top of the PDB file?
Please show me how to avoid the addition of the extra atoms HT1, HT2,
and HT3
in the patch for VAL:1.
========
applying patch FOR to 1 residues
applying patch FOR to 1 residues
no atom HN in residue VAL:1 of segment GRAA
Warning: add conformation failed in patch FOR
aliasing residue ILE atom CD1 to CD
reading coordinates from pdb file output3/gr2.pdb for segment GRAA
Info: guessing coordinates for 32 atoms (14 non-hydrogen)
Warning: poorly guessed coordinates for 34 atoms (17 non-hydrogen):
Warning: poorly guessed coordinate for atom HAY VAL:1 GRAA
Warning: poorly guessed coordinate for atom CY VAL:1 GRAA
Warning: poorly guessed coordinate for atom OY VAL:1 GRAA
Warning: poorly guessed coordinate for atom HT1 VAL:1 GRAA
Warning: poorly guessed coordinate for atom HT2 VAL:1 GRAA
Warning: poorly guessed coordinate for atom HT3 VAL:1 GRAA
Warning: poorly guessed coordinate for atom HAY VAL:18 GRAA
Warning: poorly guessed coordinate for atom CY VAL:18 GRAA
Warning: poorly guessed coordinate for atom OY VAL:18 GRAA
========
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