[AMBER] XLEaP parameters for nonstandard residues

From: Julia Blum <blum.jb1.gmail.com>
Date: Fri, 8 Jul 2011 09:05:51 -0500

Amber users and developers,

I have a protein with a phosphopantethiene group attached to a serine. To be
able to generate the mol2 and frcmod files, I have combined the
phosphopantethiene group and serine into one nonstandard residue called SRP.
I have used antechamber to create the mol2 file for it from the pdb, and
then I used parmchk to create the frcmod file. I am now having trouble
getting XLEaP to load the files correctly.

When I start XLEaP, I first source the GAFF force fields, then load the mol2
file, then load the frcmod file, then load the whole protein's pdb. When I
load the protein's pdb, XLEaP still tells me that there are unknown
parameters, residue types, bond angles, and torsions. Then, when I edit the
protein in the graphical window, I see many very long bonds and atoms with
very strange connectivity (for example, one carbon has seven bonds coming
off it). I am wondering if perhaps XLEaP has loaded the nonstandard residue
twice, thus resulting in the strange connectivities? My input into XLEaP is
shown below (I am using the ff99SB force field), and I have attached the
necessary files:

> source leaprc.gaff
> SRP = loadmol2 srp1a-edit.mol2
Loading Mol2 file: ./srp1a-edit.mol2
Reading MOLECULE named SRP
> loadamberparams srp1a-edit.frcmod
Loading parameters: ./srp1a-edit.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> 2FAE = loadpdb 2FAE-c-pf.pdb
Loading PDB file: ./2FAE-c-pf.pdb
Added missing heavy atom: .R<CASP 35>.A<OXT 13>
Created a new atom named: CA within residue: .R<SRP 36>
Created a new atom named: CB within residue: .R<SRP 36>
Created a new atom named: OG within residue: .R<SRP 36>
Created a new atom named: P24 within residue: .R<SRP 36>
Created a new atom named: S1 within residue: .R<SRP 36>
Created a new atom named: O23 within residue: .R<SRP 36>
Created a new atom named: O26 within residue: .R<SRP 36>
Created a new atom named: O27 within residue: .R<SRP 36>
Created a new atom named: C28 within residue: .R<SRP 36>
Created a new atom named: C29 within residue: .R<SRP 36>
Created a new atom named: C30 within residue: .R<SRP 36>
Created a new atom named: C31 within residue: .R<SRP 36>
Created a new atom named: C32 within residue: .R<SRP 36>
Created a new atom named: O33 within residue: .R<SRP 36>
Created a new atom named: C34 within residue: .R<SRP 36>
Created a new atom named: O35 within residue: .R<SRP 36>
Created a new atom named: N36 within residue: .R<SRP 36>
Created a new atom named: C37 within residue: .R<SRP 36>
Created a new atom named: C38 within residue: .R<SRP 36>
Created a new atom named: C39 within residue: .R<SRP 36>
Created a new atom named: O40 within residue: .R<SRP 36>
Created a new atom named: N41 within residue: .R<SRP 36>
Created a new atom named: C42 within residue: .R<SRP 36>
Created a new atom named: C43 within residue: .R<SRP 36>
  Added missing heavy atom: .R<SRP 36>.A<C11 22>
  Added missing heavy atom: .R<SRP 36>.A<O7 23>
  Added missing heavy atom: .R<SRP 36>.A<N2 24>
  Added missing heavy atom: .R<SRP 36>.A<C12 25>
  Added missing heavy atom: .R<SRP 36>.A<C13 26>
  Added missing heavy atom: .R<SRP 36>.A<S 27>
  Added missing heavy atom: .R<SRP 36>.A<C14 28>
  Added missing heavy atom: .R<SRP 36>.A<O8 29>
  Added missing heavy atom: .R<SRP 36>.A<C15 30>
  Added missing heavy atom: .R<SRP 36>.A<C16 31>
  Added missing heavy atom: .R<SRP 36>.A<C17 32>
  Added missing heavy atom: .R<SRP 36>.A<C18 33>
  Added missing heavy atom: .R<SRP 36>.A<C19 34>
  Added missing heavy atom: .R<SRP 36>.A<C20 35>
  Added missing heavy atom: .R<SRP 36>.A<C21 36>
  Added missing heavy atom: .R<SRP 36>.A<C22 37>
  Added missing heavy atom: .R<SRP 36>.A<C23 38>
  Added missing heavy atom: .R<SRP 36>.A<N1 19>
  Added missing heavy atom: .R<SRP 36>.A<O5 16>
  Added missing heavy atom: .R<SRP 36>.A<O4 10>
  Added missing heavy atom: .R<SRP 36>.A<P 8>
  Added missing heavy atom: .R<SRP 36>.A<O2 7>
  Added missing heavy atom: .R<SRP 36>.A<O3 9>
  Added missing heavy atom: .R<SRP 36>.A<O6 18>
One sided connection. Residue: missing connect1 atom.
  total atoms in file: 629
  Leap added 639 missing atoms according to residue templates:
       25 Heavy
       614 H / lone pairs
  The file contained 24 atoms not in residue templates
> check 2FAE
Checking '2FAE'....
WARNING: There is a bond of 3.600887 angstroms between:
------- .R<SRP 36>.A<C4 12> and .R<SRP 36>.A<C7 15>
WARNING: There is a bond of 7.693873 angstroms between:
------- .R<SRP 36>.A<C1 3> and .R<SRP 36>.A<O 4>
WARNING: There is a bond of 8.511503 angstroms between:
------- .R<SRP 36>.A<C 2> and .R<SRP 36>.A<C1 3>
WARNING: There is a bond of 8.998118 angstroms between:
------- .R<SRP 36>.A<C 2> and .R<SRP 36>.A<C2 5>
WARNING: The unperturbed charge of the unit: -16.994000 is not zero.
FATAL: Atom .R<SRP 36>.A<CA 84> does not have a type.
FATAL: Atom .R<SRP 36>.A<CB 85> does not have a type.
FATAL: Atom .R<SRP 36>.A<OG 86> does not have a type.
FATAL: Atom .R<SRP 36>.A<P24 87> does not have a type.
FATAL: Atom .R<SRP 36>.A<S1 88> does not have a type.
FATAL: Atom .R<SRP 36>.A<O23 89> does not have a type.
FATAL: Atom .R<SRP 36>.A<O26 90> does not have a type.
FATAL: Atom .R<SRP 36>.A<O27 91> does not have a type.
FATAL: Atom .R<SRP 36>.A<C28 92> does not have a type.
FATAL: Atom .R<SRP 36>.A<C29 93> does not have a type.
FATAL: Atom .R<SRP 36>.A<C30 94> does not have a type.
FATAL: Atom .R<SRP 36>.A<C31 95> does not have a type.
FATAL: Atom .R<SRP 36>.A<C32 96> does not have a type.
FATAL: Atom .R<SRP 36>.A<O33 97> does not have a type.
FATAL: Atom .R<SRP 36>.A<C34 98> does not have a type.
FATAL: Atom .R<SRP 36>.A<O35 99> does not have a type.
FATAL: Atom .R<SRP 36>.A<N36 100> does not have a type.
FATAL: Atom .R<SRP 36>.A<C37 101> does not have a type.
FATAL: Atom .R<SRP 36>.A<C38 102> does not have a type.
FATAL: Atom .R<SRP 36>.A<C39 103> does not have a type.
FATAL: Atom .R<SRP 36>.A<O40 104> does not have a type.
FATAL: Atom .R<SRP 36>.A<N41 105> does not have a type.
FATAL: Atom .R<SRP 36>.A<C42 106> does not have a type.
FATAL: Atom .R<SRP 36>.A<C43 107> does not have a type.
Warning: Close contact of 0.869777 angstroms between .R<ARG 6>.A<HH22 22>
and .R<SRP 36>.A<H30 69>
Warning: Close contact of 0.715219 angstroms between .R<ARG 6>.A<HH21 21>
and .R<SRP 36>.A<H31 70>
Warning: Close contact of 1.783583 angstroms between .R<ARG 6>.A<HH21 21>
and .R<SRP 36>.A<H30 69>
Warning: Close contact of 1.608639 angstroms between .R<ARG 6>.A<HH21 21>
and .R<SRP 36>.A<C17 32>
Warning: Close contact of 1.185853 angstroms between .R<ARG 6>.A<NH2 20> and
.R<SRP 36>.A<H30 69>
Warning: Close contact of 1.528207 angstroms between .R<CASP 35>.A<OXT 13>
and .R<SRP 36>.A<H1 40>
Warning: Close contact of 1.267416 angstroms between .R<CASP 35>.A<OXT 13>
and .R<SRP 36>.A<H 39>
Warning: Close contact of 0.026696 angstroms between .R<CASP 35>.A<OXT 13>
and .R<SRP 36>.A<N 1>
Warning: Close contact of 2.203725 angstroms between .R<CASP 35>.A<OXT 13>
and .R<SRP 36>.A<CA 84>
Warning: Close contact of 0.995901 angstroms between .R<CASP 35>.A<C 11> and
.R<SRP 36>.A<H 39>
Warning: Close contact of 0.551319 angstroms between .R<SRP 36>.A<H34 73>
and .R<GLU 49>.A<OE2 13>
Warning: Close contact of 2.084315 angstroms between .R<SRP 36>.A<H34 73>
and .R<GLU 49>.A<OE1 12>
Warning: Close contact of 0.584987 angstroms between .R<SRP 36>.A<H34 73>
and .R<GLU 49>.A<CD 11>
Warning: Close contact of 0.289607 angstroms between .R<SRP 36>.A<H29 68>
and .R<GLU 49>.A<HG3 10>
Warning: Close contact of 0.882974 angstroms between .R<SRP 36>.A<H29 68>
and .R<GLU 49>.A<CG 8>
Warning: Close contact of 1.787798 angstroms between .R<SRP 36>.A<H28 67>
and .R<GLU 49>.A<O 15>
Warning: Close contact of 2.176815 angstroms between .R<SRP 36>.A<H27 66>
and .R<PHE 50>.A<CZ 13>
Warning: Close contact of 1.809436 angstroms between .R<SRP 36>.A<H26 65>
and .R<PHE 50>.A<CD2 17>
Warning: Close contact of 1.580826 angstroms between .R<SRP 36>.A<H26 65>
and .R<PHE 50>.A<CE2 15>
Warning: Close contact of 2.248553 angstroms between .R<SRP 36>.A<H25 64>
and .R<PHE 50>.A<HB3 7>
Warning: Close contact of 0.257641 angstroms between .R<SRP 36>.A<H25 64>
and .R<PHE 50>.A<HB2 6>
Warning: Close contact of 0.783701 angstroms between .R<SRP 36>.A<H25 64>
and .R<PHE 50>.A<CB 5>
Warning: Close contact of 1.070653 angstroms between .R<SRP 36>.A<H23 62>
and .R<PHE 50>.A<HD1 10>
Warning: Close contact of 0.308205 angstroms between .R<SRP 36>.A<H18 57>
and .R<SRP 36>.A<O6 18>
Warning: Close contact of 1.617039 angstroms between .R<SRP 36>.A<H18 57>
and .R<SRP 36>.A<C8 17>
Warning: Close contact of 0.500469 angstroms between .R<SRP 36>.A<H15 54>
and .R<LEU 46>.A<HD13 13>
Warning: Close contact of 2.240855 angstroms between .R<SRP 36>.A<H15 54>
and .R<LEU 46>.A<HD11 11>
Warning: Close contact of 1.703112 angstroms between .R<SRP 36>.A<H15 54>
and .R<LEU 46>.A<CD1 10>
Warning: Close contact of 1.305345 angstroms between .R<SRP 36>.A<H14 53>
and .R<SRP 36>.A<H13 52>
Warning: Close contact of 0.528455 angstroms between .R<SRP 36>.A<H14 53>
and .R<SRP 36>.A<H12 51>
Warning: Close contact of 1.951937 angstroms between .R<SRP 36>.A<H14 53>
and .R<SRP 36>.A<H11 50>
Warning: Close contact of 1.354621 angstroms between .R<SRP 36>.A<H14 53>
and .R<SRP 36>.A<H8 47>
Warning: Close contact of 0.215727 angstroms between .R<SRP 36>.A<H14 53>
and .R<SRP 36>.A<C6 14>
Warning: Close contact of 0.269722 angstroms between .R<SRP 36>.A<H12 51>
and .R<SRP 36>.A<C7 15>
Warning: Close contact of 0.918804 angstroms between .R<SRP 36>.A<H11 50>
and .R<SRP 36>.A<H8 47>
Warning: Close contact of 0.506495 angstroms between .R<SRP 36>.A<H8 47> and
.R<SRP 36>.A<C6 14>
Warning: Close contact of 1.208087 angstroms between .R<SRP 36>.A<H7 46> and
.R<SRP 36>.A<H4 43>
Warning: Close contact of 1.360470 angstroms between .R<SRP 36>.A<H5 44> and
.R<SRP 36>.A<O4 10>
Warning: Close contact of 0.509818 angstroms between .R<SRP 36>.A<H4 43> and
.R<SRP 36>.A<C3 11>
Warning: Close contact of 1.004725 angstroms between .R<SRP 36>.A<H4 43> and
.R<SRP 36>.A<O4 10>
Warning: Close contact of 1.735708 angstroms between .R<SRP 36>.A<H3 42> and
.R<SRP 36>.A<S1 88>
Warning: Close contact of 2.230696 angstroms between .R<SRP 36>.A<H2 41> and
.R<SRP 36>.A<O 4>
Warning: Close contact of 1.878143 angstroms between .R<SRP 36>.A<C19 34>
and .R<GLU 49>.A<OE2 13>
Warning: Close contact of 0.659969 angstroms between .R<SRP 36>.A<C16 31>
and .R<GLU 49>.A<HG3 10>
Warning: Close contact of 1.486842 angstroms between .R<SRP 36>.A<O8 29> and
.R<PHE 50>.A<HD1 10>
Warning: Close contact of 0.989097 angstroms between .R<SRP 36>.A<O8 29> and
.R<PHE 50>.A<CD1 9>
Warning: Close contact of 0.927043 angstroms between .R<SRP 36>.A<C14 28>
and .R<PHE 50>.A<CD1 9>
Warning: Close contact of 1.278220 angstroms between .R<SRP 36>.A<C14 28>
and .R<PHE 50>.A<CG 8>
Warning: Close contact of 0.661904 angstroms between .R<SRP 36>.A<S 27> and
.R<PHE 50>.A<CG 8>
Warning: Close contact of 0.748070 angstroms between .R<SRP 36>.A<C13 26>
and .R<PHE 50>.A<HB2 6>
Warning: Close contact of 1.550696 angstroms between .R<SRP 36>.A<C13 26>
and .R<PHE 50>.A<CB 5>
Warning: Close contact of 1.977905 angstroms between .R<SRP 36>.A<O7 23> and
.R<ILE 72>.A<HG12 12>
Warning: Close contact of 2.013000 angstroms between .R<SRP 36>.A<C9 20> and
.R<SRP 36>.A<O6 18>
Warning: Close contact of 0.024610 angstroms between .R<SRP 36>.A<O4 10> and
.R<SRP 36>.A<C2 5>
Warning: Close contact of 1.433496 angstroms between .R<SRP 36>.A<O3 9> and
.R<SRP 36>.A<O1 6>
Warning: Close contact of 1.951559 angstroms between .R<SRP 36>.A<P 8> and
.R<SRP 36>.A<C2 5>
Warning: Close contact of 0.237181 angstroms between .R<SRP 36>.A<P 8> and
.R<SRP 36>.A<C1 3>
Warning: Close contact of 1.364560 angstroms between .R<SRP 36>.A<C 2> and
.R<LEU 37>.A<H 2>
Checking parameters for unit '2FAE'.
Checking for bond parameters.
Could not find bond parameter for: C - n3
Could not find bond parameter for: c -
Could not find bond parameter for: c3 -
Could not find bond parameter for: c3 - N
Could not find bond parameter for: n3 -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Could not find bond parameter for: -
Checking for angle parameters.
Could not find angle parameter: O2 - C - n3
Could not find angle parameter: O2 - C - n3
Could not find angle parameter: C - n3 - c3
Could not find angle parameter: C - n3 - hn
Could not find angle parameter: C - n3 - hn
Could not find angle parameter: C - n3 -
Could not find angle parameter: CT - C - n3
Could not find angle parameter: h4 - c -
Could not find angle parameter: h1 - c3 -
Could not find angle parameter: h1 - c3 - N
Could not find angle parameter: hn - n3 -
Could not find angle parameter: hn - n3 -
Could not find angle parameter: os - c - h4
Could not find angle parameter: os - c -
Could not find angle parameter: c3 - c3 -
Could not find angle parameter: c3 - c3 - N
Could not find angle parameter: c3 - c -
Could not find angle parameter: o - c -
Could not find angle parameter: o - c3 -
Could not find angle parameter: o - c3 - N
Could not find angle parameter: c - c3 -
Could not find angle parameter: c - c3 - o
Could not find angle parameter: c - c3 - N
Could not find angle parameter: c - -
Could not find angle parameter: c3 - n3 -
Could not find angle parameter: c3 - c -
Could not find angle parameter: c3 - -
Could not find angle parameter: c3 - o - c
Could not find angle parameter: c3 - N - H
Could not find angle parameter: c3 - N - CT
Could not find angle parameter: n3 - c3 -
Could not find angle parameter: n3 - c3 - o
Could not find angle parameter: n3 - c3 - N
Could not find angle parameter: n3 - - c3
Could not find angle parameter: n3 - -
Could not find angle parameter: - c3 - N
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
Could not find angle parameter: - -
There are missing parameters.
check: Errors: 24 Warnings: 63

I realize that all this has something to do with the way I have defined the
SRP residue before loading the protein with the SRP residue in it, but I
can't figure out a way to fix this. Your help and suggestions would be
greatly appreciated!

-Julia


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Received on Fri Jul 08 2011 - 07:30:04 PDT
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