Dear Amber users,
the object is quite self-explanatory: I have a protein (crystallographic
structure from the PDB) where a loop is missing, and I would like to cap
the ends with ACE and NME. I tried to do it with Molden, but then Leap
cannot recognize the atom type!!
This is the *PDB* file I'm loading in tLeap:
...
ATOM 902 HB3 ASP A 57 37.567 41.833 26.643 1.00 36.04
H
ATOM 903 N NME A 58 36.230 44.950 26.150 1.00 0.00
ATOM 904 CH3 NME A 58 35.500 45.900 25.320 1.00 0.00
ATOM 905 HN2 NME A 58 37.215 45.191 26.258 1.00 0.00
H
ATOM 906 H1 NME A 58 36.178 46.684 24.983 1.00 0.00
H
ATOM 907 H2 NME A 58 35.084 45.383 24.455 1.00 0.00
H
ATOM 908 H3 NME A 58 34.691 46.344 25.900 1.00 0.00
H
TER
ATOM 909 CH3 ACE B 59 43.550 44.870 17.830 1.00 0.00
ATOM 910 C ACE B 59 44.710 43.880 17.790 1.00 0.00
ATOM 911 O ACE B 59 45.780 44.190 18.310 1.00 0.00
ATOM 912 H1 ACE B 59 43.252 45.123 16.812 1.00 0.00
H
ATOM 913 H2 ACE B 59 42.706 44.421 18.354 1.00 0.00
H
ATOM 914 H3 ACE B 59 43.862 45.775 18.352 1.00 0.00
H
ATOM 915 N ILE B 60 44.597 42.703 17.173 1.00 30.43
N
...
This is the *leap input*:
*source leaprc.constphrho = loadPDB rho.pdbsaveAmberParm rho rho.parm7
rho.rst7quit*
And this is the* leap.log* (final part; complete file in attachment):
...
Loading PDB file: ./rho.pdb
Created a new atom named: HCA within residue: .R<GL4 36>
Created a new atom named: HN2 within residue: .R<NME 58>
Created a new atom named: H1 within residue: .R<NME 58>
Created a new atom named: H2 within residue: .R<NME 58>
Created a new atom named: H3 within residue: .R<NME 58>
Created a new atom named: H1 within residue: .R<ACE 59>
Created a new atom named: H2 within residue: .R<ACE 59>
Created a new atom named: H3 within residue: .R<ACE 59>
total atoms in file: 3546
Leap added 94 missing atoms according to residue templates:
94 H / lone pairs
The file contained 8 atoms not in residue templates
Checking Unit.
WARNING: The unperturbed charge of the unit: 7.000000 is not zero.
FATAL: Atom .R<GL4 36>.A<HCA 20> does not have a type.
FATAL: Atom .R<NME 58>.A<HN2 7> does not have a type.
FATAL: Atom .R<NME 58>.A<H1 8> does not have a type.
FATAL: Atom .R<NME 58>.A<H2 9> does not have a type.
FATAL: Atom .R<NME 58>.A<H3 10> does not have a type.
FATAL: Atom .R<ACE 59>.A<H1 7> does not have a type.
FATAL: Atom .R<ACE 59>.A<H2 8> does not have a type.
FATAL: Atom .R<ACE 59>.A<H3 9> does not have a type.
Failed to generate parameters
Parameter file was not saved.
Quit
How can I solve this?
Elisa
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Received on Fri Jan 22 2016 - 05:30:07 PST
