What is the residue name defined in srp1a-edit.mol2 file? Also, are the
atom names in the .pdb file the same as it is defined in srp1a-edit.mol2?
If the residue name in the .mol2 file is SRP, then just directly load it
as "loadmol2 srp1a-edit.mol2".
Ilyas Yildirim, Ph.D.
-----------------------------------------------------------
= Department of Chemistry - 2145 Sheridan Road =
= Northwestern University - Evanston, IL 60208 =
= Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
=
http://www.pas.rochester.edu/~yildirim/ =
-----------------------------------------------------------
On Fri, 8 Jul 2011, Julia Blum wrote:
> 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 - 08:00:03 PDT
