Thank you Vasantha!
Indeed, looking in the AmberTools15 manual for other stuff, I randomly
found out that ACE and NME terminal caps are "special", meaning that
hydrogens should be omitted for them: pag 192.
To sum up, I just removed those lines and everything looks fine now.
For the GLH problem, for some reason when I added the hydrogens using the
command:
pdb4amber -i 1XIO.pdb -o rho.pdb --dry --reduce
for some reason, the HA hydrogen was labelled as HCA, so I just removed the
"C". But I have no idea of the reason of this.
Anyway..thanks again!
Elisa
On Fri, Jan 22, 2016 at 3:37 PM, Vasantha Kumar <vin.vasanth.gmail.com>
wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Fri Jan 22 2016 - 07:30:03 PST
