[gmx-users] Adding modified nucleotide to a forcefield
Justin A. Lemkul
jalemkul at vt.edu
Fri Feb 4 04:44:48 CET 2011
william Stebbeds wrote:
> Thanks again,
>
> You were right, it was a misaligned pdb file :).
>
> However I now get an error when I use grompp:
>
> ERROR 1 [file newoxi.noNaCl_DNA.itp, line 1381]:
> No default Bond types
>
>
> ERROR 2 [file newoxi.noNaCl_DNA.itp, line 4462]:
> No default Angle types
>
>
> ERROR 3 [file newoxi.noNaCl_DNA.itp, line 4464]:
> No default Angle types
>
>
> ERROR 4 [file newoxi.noNaCl_DNA.itp, line 6919]:
> No default Improper Dih. types
>
> My assumption is that I have not set the angles and dihedrals properly
> but have rechecked the rtp entry and all seems to be correct.
>
The errors indicate that you've specified bonded parameters that do not exist in
the force field. Look into the referenced .itp file at those lines, map back
the atoms in question, and identify which terms they correspond to. If you
don't find matching entries in ffbonded.itp, then either you have to derive them
yourself or find suitable parameters for them.
-Justin
> Once Again thank you for helping out a gromacs newbie.
>
>
>
> > Date: Thu, 3 Feb 2011 20:43:24 -0500
> > From: jalemkul at vt.edu
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Adding modified nucleotide to a forcefield
> >
> >
> >
> > william Stebbeds wrote:
> > > Thanks for the reply,
> > >
> > > ffamber99sb.rtp entry:
> > > [ DGO ]
> > > [ atoms ]
> > > P amber99_46 1.16590 1
> > > O1P amber99_45 -0.77610 2
> > > O2P amber99_45 -0.77610 3
> > > O5' amber99_44 -0.49540 4
> > > C5' amber99_11 -0.00690 5
> > > H5'1 amber99_19 0.07540 6
> > > H5'2 amber99_19 0.07540 7
> > > C4' amber99_11 0.16290 8
> > > H4' amber99_19 0.11760 9
> > > O4' amber99_44 -0.36910 10
> > > C1' amber99_11 0.03580 11
> > > H1' amber99_20 0.17460 12
> > > N9 amber99_40 0.05770 13
> > > C8 amber99_6 0.07360 14
> > > O8 amber99_44 -0.36910 15
> > > N7 amber99_36 -0.57250 16
> > > C5 amber99_4 0.19910 17
> > > C6 amber99_2 0.49180 18
> > > O6 amber99_41 -0.56990 19
> > > N1 amber99_35 -0.50530 20
> > > H1 amber99_17 0.35200 21
> > > C2 amber99_3 0.74320 22
> > > N2 amber99_38 -0.92300 23
> > > H21 amber99_17 0.42350 24
> > > H22 amber99_17 0.42350 25
> > > N3 amber99_37 -0.66360 26
> > > C4 amber99_4 0.18140 27
> > > C3' amber99_11 0.07130 28
> > > H3' amber99_19 0.09850 29
> > > C2' amber99_11 -0.08540 30
> > > H2'1 amber99_18 0.07180 31
> > > H2'2 amber99_18 0.07180 32
> > > O3' amber99_44 -0.52320 33
> > > [ bonds ]
> > > P O1P
> > > P O2P
> > > P O5'
> > > O5' C5'
> > > C5' H5'1
> > > C5' H5'2
> > > C5' C4'
> > > C4' H4'
> > > C4' O4'
> > > C4' C3'
> > > O4' C1'
> > > C1' H1'
> > > C1' N9
> > > C1' C2'
> > > N9 C8
> > > N9 C4
> > > C8 O8
> > > C8 N7
> > > N7 C5
> > > C5 C6
> > > C5 C4
> > > C6 O6
> > > C6 N1
> > > N1 H1
> > > N1 C2
> > > C2 N2
> > > C2 N3
> > > N2 H21
> > > N2 H22
> > > N3 C4
> > > C3' H3'
> > > C3' C2'
> > > C3' O3'
> > > C2' H2'1
> > > C2' H2'2
> > > -O3' P
> > > [ dihedrals ]
> > > O4' C1' N9 C4 proper_X_CT_N*_X
> > > C1' N9 C8 O8 proper_X_CK_N*_X
> > > C1' N9 C8 N7 proper_X_CK_N*_X
> > > C1' N9 C4 C5 proper_X_CB_N*_X
> > > C1' N9 C4 N3 proper_X_CB_N*_X
> > > H1' C1' N9 C8 proper_X_CT_N*_X
> > > H1' C1' N9 C4 proper_X_CT_N*_X
> > > C8 N9 C4 C5 proper_X_CB_N*_X
> > > C8 N9 C4 N3 proper_X_CB_N*_X
> > > C5 C6 N1 H1 proper_X_C_NA_X
> > > C5 C6 N1 C2 proper_X_C_NA_X
> > > C6 N1 C2 N2 proper_X_CA_NA_X
> > > C6 N1 C2 N3 proper_X_CA_NA_X
> > > O6 C6 N1 H1 proper_X_C_NA_X
> > > O6 C6 N1 C2 proper_X_C_NA_X
> > > N1 C2 N3 C4 proper_X_CA_NC_X
> > > H1 N1 C2 N2 proper_X_CA_NA_X
> > > H1 N1 C2 N3 proper_X_CA_NA_X
> > > N2 C2 N3 C4 proper_X_CA_NC_X
> > > H8 C8 N7 C5 proper_X_CK_NB_X
> > > N9 C8 N7 C5 proper_X_CK_NB_X
> > > H8 C8 N9 C4 proper_X_CK_N*_X
> > > N7 C8 N9 C4 proper_X_CK_N*_X
> > > O4' C1' C2' H2'1 proper_H_CT_CT_O
> > > O4' C1' C2' H2'2 proper_H_CT_CT_O
> > > O3' C3' C2' H2'1 proper_H_CT_CT_O
> > > O3' C3' C2' H2'2 proper_H_CT_CT_O
> > > [ impropers ]
> > > C4 C8 N9 C1' nucleic_imp_10
> > > C5 N1 C6 O6
> > > C6 C2 N1 H1 nucleic_imp_10
> > > C2 H21 N2 H22
> > > N9 N7 C8 O8
> > > N2 N1 C2 N3 nucleic_imp_11
> > >
> > > DGO was also added to residuetypes.dat. hdb file was also updated, as
> > > was dna.rtp within amber99sb.ff.
> > >
> > > The problem is not a simple missing bond, as when the structure goes
> > > through pdb2gmx, the new nucleotide appears on the other side of the
> > > pbc, in a straight line (i.e. without form).
> > >
> >
> > As in, the atoms of DGO are visually a straight line? That would be a
> > consequence of an incorrectly-formatted input file. If you're using a
> .pdb
> > file, it's fixed-format, so any incorrect spacing will screw up the
> coordinates.
> >
> > To clarify, are you missing a bond, as your first message would
> imply? I can
> > see how you might be missing bonds; your residue definition doesn't
> specify a
> > bond to the next nucleotide (i.e. "O3' +P"), although if it's a 3'
> ending
> > nucleotide, this wouldn't apply. If it's an internal residue, you may
> also be
> > missing necessary dihedral definitions as well.
> >
> > -Justin
> >
> > > Thanks
> > >
> > > Will
> > >
> > > > Date: Thu, 3 Feb 2011 16:07:42 -0500
> > > > From: jalemkul at vt.edu
> > > > To: gmx-users at gromacs.org
> > > > Subject: Re: [gmx-users] Adding modified nucleotide to a forcefield
> > > >
> > > >
> > > >
> > > > william Stebbeds wrote:
> > > > > Hello,
> > > > >
> > > > > I am attempting to add 8-oxo-dG (8-Oxo-2'-deoxyguanosine) to the
> > > > > amber99sb force field. This is a simple modification of the H8
> > > hydrogen
> > > > > on a guanine to an oxygen atom. I have followed the
> instructions on
> > > the
> > > > > gromacs site on adding residues.
> > > > >
> > > > > However the new nucleotide will not work, it will not attach to the
> > > > > adjacent nucleotides in the sequence.
> > > > >
> > > >
> > > > So a bond is missing?
> > > >
> > > > > Any help would be very much appreciated, if any more information is
> > > > > required please let me know.
> > > > >
> > > >
> > > > A lot more information is needed, at the very least, your .rtp entry.
> > > >
> > > > -Justin
> > > >
> > > > > Best Regards
> > > > >
> > > > > William Stebbeds
> > > > > Cranfield University
> > > > > UK
> > > > >
> > > >
> > > > --
> > > > ========================================
> > > >
> > > > Justin A. Lemkul
> > > > Ph.D. Candidate
> > > > ICTAS Doctoral Scholar
> > > > MILES-IGERT Trainee
> > > > Department of Biochemistry
> > > > Virginia Tech
> > > > Blacksburg, VA
> > > > jalemkul[at]vt.edu | (540) 231-9080
> > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > > >
> > > > ========================================
> > > > --
> > > > gmx-users mailing list gmx-users at gromacs.org
> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > > Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > > Please don't post (un)subscribe requests to the list. Use the
> > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
More information about the gromacs.org_gmx-users
mailing list