Dear Nikolay,
So it looks like the saga continues ;-)
A) About the LEaP program:
- when you load a set of FF libraries and a PDB file representing your
macromolecular system in LEaP, each different residue belonging to the
PDB file has to be represented by a FF library.
- Concerning the notion of residue, (1) a FF library must contain all
the atoms of that residue, while some atoms might be missing of that
residue in the PDB file (LEaP adds the missing atoms based on these in
the FF lib). (2) The atom names and residue name present in the PDB
file must exactly match these in the FF library.
B) These rules being remembered are you sure that Antechamber does
handle molecular fragments?
A fragment is different from a whole molecule; see:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#2
Old Antechamber versions? the answer was no: Antechamber did not
handle molecular fragments - only whole molecules.
Indeed in your case you likely need a central molecular fragment for
your modified amino-acid as described in:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#16
This is why I suggested you to use PyRED at R.E.D. Server Dev.:
http://q4md-forcefieldtools.org/REDServer-Development
and to read the tutorial at:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.ph
C) A last point:
Using the .lib (i.e. off) or .in (i.e. prep) file formats for a FF
library is, all, but friendly...
See
http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
This is why we have introduced some commands related to the mol2 file
format for whole molecules and mol3 file format for molecular
fragments in LEaP...
I hope this helps a little bit...
regards, Francois
Quoting "Nikolay N. Kuzmich" <nnkuzmich.gmail.com>:
> Dear Abhishek and Amber users,
>
> what is wrong with the proline oxygen atom of the C-tail then?
>
> Kind regards,
> Nick
>
> Subject: Re: [AMBER] Simulating a protein with modified amino acid
> residue, the saga continues. Atom ... does not have a type.
> To: "amber.ambermd.org" <amber.ambermd.org>
> Message-ID:
> <BY2PR07MB6298ED0C50011CF454609B09E2C0.BY2PR07MB629.
> namprd07.prod.outlook.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> HI Nick,
>
> you will have to make a separate ADF.frcmod and AFR.lib file and
> incorporate that while making prmtop file for you complex system.
>
> Also make sure that if there is bond between ADF and TYR then you need a
> parameter files for that specific bond too.
>
>
>
>
> ________________________________
> From: Nikolay N. Kuzmich <nnkuzmich.gmail.com>
> Sent: Monday, March 6, 2017 6:16:33 AM
> To: amber.ambermd.org
> Subject: [AMBER] Simulating a protein with modified amino acid residue, the
> saga continues. Atom ... does not have a type.
>
> Dear Amber users,
>
> I have prepared protein with a modified amino acid residue for MD
> simulation.
> The amino acid was modified and the 2 amino acids L and P missing on the
> C-tails were added manually using Schrodinger/Maestro. Protonation was also
> performed there.
> Some HIS and ASP in the PDB were modified taking into account Amber
> requirements and transformed into HID, HIP and ASH. The modified amino acid
> residue (ADF) was prepared using Antechamber, the prepin and frcmod files
> have been generated. In the xLeap I loaded the PDB file and tried to obtain
> prmtop and inpcrd files for simulation, but I had the error messages:
>
>> saveamberparm DP_Inh1 DP_Inh1.prmtop DP_Inh1.inpcrd
> Checking Unit.
> WARNING: There is a bond of 3.465406 angstroms between:
> ------- .R<TRP 629>.A<C 23> and .R<ADF 630>.A<O 1>
> WARNING: There is a bond of 3.670118 angstroms between:
> ------- .R<ADF 630>.A<C13 32> and .R<TYR 631>.A<N 1>
> WARNING: There is a bond of 3.253292 angstroms between:
> ------- .R<ADF 630>.A<N30 7> and .R<ADF 630>.A<H 8>
> FATAL: Atom .R<ADF 630>.A<N 35> does not have a type.
> FATAL: Atom .R<ADF 630>.A<C 36> does not have a type.
> FATAL: Atom .R<CPRO 766>.A<O1 16> does not have a type.
> FATAL: Atom .R<CPRO 1494>.A<O1 16> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
> I checked the PDB file in Maestro visually and found no discrepancies or
> absent atoms.
> Here are the fragments from the leap.log file:
> ...
>
> Joining TRP - ADF
> Created a new atom named: N within residue: .R<ADF 630>
> Created a new atom named: C within residue: .R<ADF 630>
> Added missing heavy atom: .R<ADF 630>.A<N30 7>
> Added missing heavy atom: .R<ADF 630>.A<C32 2>
> Added missing heavy atom: .R<ADF 630>.A<O33 3>
> failed to find default bond length N-C13, types N-c3
> Joining ADF - TYR
>
> ...
>
> Joining LEU - CPRO
> Created a new atom named: O1 within residue: .R<CPRO 766>
> Added missing heavy atom: .R<CPRO 766>.A<OXT 15>
>
> ...
>
> Joining LEU - CPRO
> Created a new atom named: O1 within residue: .R<CPRO 1494>
> Added missing heavy atom: .R<CPRO 1494>.A<OXT 15>
> total atoms in file: 23334
> Leap added 30 missing atoms according to residue templates:
> 5 Heavy
> 24 H / lone pairs
> 1 unknown element
> The file contained 4 atoms not in residue templates
> *The problem residues in the PDB:*
>
> HETATM23306 N ADF A 630 6.272 -4.170 -4.285 1.00
> 42.06 N
> HETATM23307 CA ADF A 630 5.879 -2.815 -3.942 1.00
> 42.06 C
> HETATM23308 C ADF A 630 7.111 -1.871 -3.989 1.00
> 42.06 C
> HETATM23309 O ADF A 630 7.710 -1.803 -5.247 1.00
> 42.06 O
> HETATM23310 CB ADF A 630 5.206 -2.825 -2.581 1.00
> 42.06 C
> HETATM23311 OG ADF A 630 4.738 -1.530 -2.371 1.00
> 42.06 O
> HETATM23312 C1 ADF A 630 3.393 1.132 0.971 1.00
> 42.06 C
> HETATM23313 O3 ADF A 630 2.690 0.134 1.093 1.00
> 42.06 O
> HETATM23314 N8 ADF A 630 4.128 1.390 -0.138 1.00
> 42.06 N
> HETATM23315 C12 ADF A 630 4.151 0.574 -1.367 1.00
> 42.06 C
> HETATM23316 C13 ADF A 630 5.064 1.331 -2.351 1.00
> 42.06 C
> HETATM23317 C14 ADF A 630 5.841 2.327 -1.391 1.00
> 42.06 C
> HETATM23318 C15 ADF A 630 4.603 2.670 -0.279 1.00
> 42.06 C
> HETATM23319 C21 ADF A 630 4.790 -0.824 -1.230 1.00
> 42.06 C
> HETATM23320 N22 ADF A 630 5.326 -1.273 -0.080 1.00
> 42.06 N
> HETATM23321 C2 ADF A 630 3.865 3.212 1.173 1.00
> 0.00 C
> HETATM23322 N1 ADF A 630 3.607 2.034 1.963 1.00
> 0.00 N
> HETATM23323 H ADF A 630 5.821 -4.628 -5.064 1.00
> 0.00 H
> HETATM23324 HA ADF A 630 5.155 -2.471 -4.680 1.00
> 0.00 H
> HETATM23325 HB3 ADF A 630 5.941 -3.073 -1.815 1.00
> 0.00 H
> HETATM23326 HB2 ADF A 630 4.363 -3.516 -2.599 1.00
> 0.00 H
> HETATM23327 H12 ADF A 630 3.147 0.486 -1.782 1.00
> 0.00 H
> HETATM23328 H131 ADF A 630 4.451 1.908 -3.043 1.00
> 0.00 H
> HETATM23329 H132 ADF A 630 5.722 0.622 -2.853 1.00
> 0.00 H
> HETATM23330 H141 ADF A 630 6.113 3.181 -2.077 1.00
> 0.00 H
> HETATM23331 H142 ADF A 630 6.767 1.749 -1.117 1.00
> 0.00 H
> HETATM23332 H15 ADF A 630 4.121 3.125 -1.074 1.00
> 0.00 H
> HETATM23333 HN22 ADF A 630 5.329 -0.683 0.740 1.00
> 0.00 H
> HETATM23334 H1 ADF A 630 2.823 3.725 1.188 1.00
> 0.00 H
> HETATM23335 H2 ADF A 630 4.234 3.654 2.073 1.00
> 0.00 H
> HETATM23336 H3 ADF A 630 3.479 1.869 3.024 1.00
> 0.00 H
>
> ATOM 11632 N PRO A 766 17.819 -22.728 -20.538 1.00
> 0.00 N
> ATOM 11633 CA PRO A 766 16.808 -22.938 -21.308 1.00
> 0.00 C
> ATOM 11634 C PRO A 766 16.557 -22.705 -22.777 1.00
> 0.00 C
> ATOM 11635 O PRO A 766 17.448 -22.595 -23.414 1.00
> 0.00 O
> ATOM 11636 O1 PRO A 766 15.304 -22.458 -23.180 1.00
> 0.00 O1-
> ATOM 11637 CD PRO A 766 17.534 -21.460 -19.970 1.00
> 0.00 C
> ATOM 11638 CB PRO A 766 15.352 -21.766 -20.525 1.00
> 0.00 C
> ATOM 11639 CG PRO A 766 16.219 -20.816 -20.388 1.00
> 0.00 C
> ATOM 11640 HA PRO A 766 16.127 -24.099 -20.910 1.00
> 0.00 H
> ATOM 11641 HD3 PRO A 766 17.510 -21.668 -18.900 1.00
> 0.00 H
> ATOM 11642 HD2 PRO A 766 18.362 -20.818 -20.270 1.00
> 0.00 H
> ATOM 11643 HB2 PRO A 766 14.564 -21.723 -21.395 1.00
> 0.00 H
> ATOM 11644 HB3 PRO A 766 14.977 -22.437 -19.738 1.00
> 0.00 H
> ATOM 11645 HG2 PRO A 766 16.372 -20.253 -21.308 1.00
> 0.00 H
> ATOM 11646 HG3 PRO A 766 15.811 -20.302 -19.625 1.00
> 0.00 H
> TER 11647 PRO A 766
>
>
> ATOM 23290 N PRO B 766 14.978 -24.608 -24.748 1.00
> 0.00 N
> ATOM 23291 CA PRO B 766 15.228 -23.875 -23.839 1.00
> 0.00 C
> ATOM 23292 C PRO B 766 15.367 -24.024 -22.215 1.00
> 0.00 C
> ATOM 23293 O PRO B 766 15.617 -25.050 -21.948 1.00
> 0.00 O
> ATOM 23294 O1 PRO B 766 15.214 -23.105 -21.364 1.00
> 0.00 O1-
> ATOM 23295 CD PRO B 766 13.582 -24.459 -24.886 1.00
> 0.00 C
> ATOM 23296 CB PRO B 766 13.772 -22.469 -23.734 1.00
> 0.00 C
> ATOM 23297 CG PRO B 766 12.897 -23.487 -23.936 1.00
> 0.00 C
> ATOM 23298 HA PRO B 766 16.147 -22.770 -24.231 1.00
> 0.00 H
> ATOM 23299 HD3 PRO B 766 13.471 -24.102 -25.910 1.00
> 0.00 H
> ATOM 23300 HD2 PRO B 766 13.182 -25.460 -24.730 1.00
> 0.00 H
> ATOM 23301 HB2 PRO B 766 13.805 -22.004 -22.690 1.00
> 0.00 H
> ATOM 23302 HB3 PRO B 766 14.064 -21.782 -24.503 1.00
> 0.00 H
> ATOM 23303 HG2 PRO B 766 12.647 -24.006 -23.011 1.00
> 0.00 H
> ATOM 23304 HG3 PRO B 766 12.128 -23.029 -24.380 1.00
> 0.00 H
> TER 23305 PRO B 766
>
> What should I do/edit in the PDB file for xLeap not to complain?
>
> Thank you in advance,
>
> Nick
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Fri Mar 10 2017 - 10:00:02 PST
