[gmx-users] lactam bridge problems
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 1 19:57:43 CET 2011
Jerez Te wrote:
>
> I want to create a peptide bond between glu and lys using Gromacs
> 4.5.3. One option that I have is to modify the topology file (bonds,
> angles, etc.) but I also want to do a number of these lactam bridges
> so it is a pain to make the bonds, delete the atoms in glu and lys
> that are not needed and renumber the .itp and .gro files.
>
> The other option is to add the lactam glu (LCE) and lactam lys (LCK)
> as residues to the force field. So far I have added LCE and LCK to
> gromos53a6 and opls-aa but i always get the same error: "Atom HZ1
> not found in rtp database in residue LCK, it looks a bit like HZ" -
> there is no HZ1 in all my files but pdb2gmx seem to be looking for it.
>
> The naming is consistent (HZ is specified in the .rtp files, in the
> pdb file). Here are the modiifcation that I made involving gromos53a6.
>
> Following the "Adding a residue to a force field section" in the
> gromacs website
> 1.)
> -------- In aminoacids.rtp (I'm just showing LCK)
> [ LCK ]
> [ atoms ]
> N N -0.31000 0
> H H 0.31000 0
> CA CH1 0.00000 1
> CB CH2 0.00000 1
> CG CH2 0.00000 2
> CD CH2 0.00000 2
> CE CH2 0.00000 3
> NZ N -0.31000 3 ; same atom type as amide N
> HZ H 0.31000 3 ; same atom type as amide H
> C C 0.450 4
> O O -0.450 4
> [ bonds ]
> N H gb_2
> N CA gb_21
> CA CB gb_27
> CA C gb_27
> CB CG gb_27
> CG CD gb_27
> CD CE gb_27
> CE NZ gb_21 ; same bond as N-CA
> NZ HZ gb_2 ; same bond as N-H
> C O gb_5
> C +N gb_10
> [ angles ]
> ; ai aj ak gromos type
> -C N H ga_32
> -C N CA ga_31
> H N CA ga_18
> N CA CB ga_13
> N CA C ga_13
> CB CA C ga_13
> CA CB CG ga_15
> CB CG CD ga_15
> CG CD CE ga_15
> CD CE NJ ga_15
> CE NJ HJ ga_31
> CA C O ga_30
> CA C +N ga_19
> O C +N ga_33
> [ impropers ]
> ; ai aj ak al gromos type
> N -C CA H gi_1
> CA N C CB gi_2
> C CA +N O gi_1
> [ dihedrals ]
> ; ai aj ak al gromos type
> -CA -C N CA gd_14
> -C N CA C gd_39
> N CA CB CG gd_34
> N CA C +N gd_40
> CA CB CG CD gd_34
> CB CG CD CE gd_34
> CG CD CE NJ gd_34
> CD CE NJ HJ gd_29
>
> 2.) HBD has been update
> LCK 2
> 1 1 H N -C CA
> 2 4 HZ NZ CE CD
>
> 3.) no new atom types introduced atomtypes.atp and ffnonbonded.itp
> not modified. Note: I did try introducing new atom types in a
> previous attempt (not on this attempt) but I still get the same
> error above.
>
> 4.) no new bond types introduced (ffbonded.itp is not modified).
>
> 5.) In residuetypes.dat (the new residues were declared)
> LCK Protein
> LCE Protein
>
> 6.) specbond.dat (the peptide bond was introduced)
> LCE CD 1 LCK NZ 1 0.133 LCTM LCTM
>
> It seems like pdb2gmx is still looking at my new residues as if they
> were lys and glu and that might be the source of the error (In my
> original pdb file, LCE and LCK were used so the error does not come
> from there and the atom names are also consistent).
> Here's a portion of the pdb file that I used:
>
> ATOM 1759 N LCK B 20 -3.985 -0.668 6.218 1.00
> 20.00 N
> ATOM 1760 CA LCK B 20 -3.534 -1.515 5.127 1.00
> 20.00 C
> ATOM 1761 C LCK B 20 -2.096 -1.976 5.372 1.00
> 20.00 C
> ATOM 1762 O LCK B 20 -1.823 -3.174 5.413 1.00
> 20.00 O
> ATOM 1763 HA LCK B 20 -4.173 -2.398 5.113 1.00
> 20.00 H
> ATOM 1764 CB LCK B 20 -3.662 -0.780 3.790 1.00
> 20.00 C
> ATOM 1765 1HB LCK B 20 -4.701 -0.500 3.623 1.00
> 20.00 H
> ATOM 1766 2HB LCK B 20 -3.084 0.143 3.823 1.00
> 20.00 H
> ATOM 1767 CG LCK B 20 -3.171 -1.655 2.635 1.00
> 20.00 C
> ATOM 1768 1HG LCK B 20 -2.125 -1.918 2.792 1.00
> 20.00 H
> ATOM 1769 2HG LCK B 20 -3.735 -2.588 2.616 1.00
> 20.00 H
> ATOM 1770 CD LCK B 20 -3.326 -0.932 1.296 1.00
> 20.00 C
> ATOM 1771 1HD LCK B 20 -3.061 0.119 1.413 1.00
> 20.00 H
> ATOM 1772 2HD LCK B 20 -2.635 -1.356 0.567 1.00
> 20.00 H
> ATOM 1773 CE LCK B 20 -4.760 -1.047 0.774 1.00
> 20.00 C
> ATOM 1774 1HE LCK B 20 -4.973 -2.081 0.503 1.00
> 20.00 H
> ATOM 1775 2HE LCK B 20 -5.463 -0.771 1.560 1.00
> 20.00 H
> ATOM 1776 NZ LCK B 20 -4.955 -0.170 -0.403 1.00
> 20.00 N
> ATOM 1777 HZ LCK B 20 -5.909 -0.258 -0.736 1.00
> 20.00 H
> ATOM 1778 HN LCK B 20 -3.255 -0.255 6.762 1.00
> 20.00 H
>
> Any suggestion as to how to solve this error?
>
I will assume that you're using -ignh with pdb2gmx? Otherwise, you'd be getting
a fatal error about about HN not being found in the .rtp entry. You've
constructed your .hdb file such that pdb2gmx is going to try to add 2 HZ atoms
(thus HZ1 and HZ2), and hence the fatal error.
-Justin
--
========================================
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
========================================
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