Ciao Elisa
Have you considered to changing the atom name for ACE and NME (from
molden) to standard atoms in amber library for ACE and NME.?
Residue name in correct and atom name in it do not match ACE and NME libs
in AMBER. May be change atom in amber format..
1 N 3.325770 1.547909 -0.000002 N 1 NME -0.4157
2 H 3.909407 0.723611 -0.000003 H 1 NME 0.2719
3 CH3 3.970048 2.845795 -0.000000 CT 1 NME -0.1490
4 HH31 3.211504 3.628554 0.000002 H1 1 NME 0.0976
5 HH32 4.591993 2.943271 0.889822 H1 1 NME 0.0976
6 HH33 4.591988 2.943275 -0.889825 H1 1 NME 0.0976
1 HH31 2.000001 1.000000 -0.000001 HC 1 ACE 0.1123
2 CH3 2.000001 2.090000 0.000000 CT 1 ACE -0.3662
3 HH32 1.486264 2.453849 0.889824 HC 1 ACE 0.1123
4 HH33 1.486259 2.453852 -0.889820 HC 1 ACE 0.1123
5 C 3.427420 2.640795 -0.000003 C 1 ACE 0.5972
6 O 4.390580 1.877406 -0.000007 O 1 ACE -0.5679
Ciao!!!
Vasatha
On 22 January 2016 at 14:20, Elisa Pieri <elisa.pieri90.gmail.com> wrote:
> 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 - 07:00:05 PST
