Dear Nick,
The saga continues? :-)
Well see
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#16
I would use PyRED at R.E.D. Server Dev.:
http://q4md-forcefieldtools.org/REDServer-Development/
I hope that saga will be shortened...
regards, Francois
Quoting "Nikolay N. Kuzmich" <nnkuzmich.gmail.com>:
> 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 Tue Mar 07 2017 - 02:00:02 PST
