[gmx-users] Adding HSD residue to AMBER ff99SB-ILDN

[Simone Bolognini]

Well... that was a rookie mistake. Sorry about that. Thank you!

Il giorno gio 20 ago 2015 alle ore 14:18 Justin Lemkul <jalemkul at vt.edu> ha
scritto:

>
>
> On 8/20/15 8:16 AM, Simone Bolognini wrote:
> > Thank you for your answer! I did it and now gromacs throws me the
> following
> > error: "Atom HG1 in residue SER 2 was not found in rtp entry SER with 11
> > atoms while sorting atoms.". Any clue? Thank you very much.
> >
>
> pdb2gmx -ignh
>
> -Justin
>
> > Il giorno gio 20 ago 2015 alle ore 13:18 Justin Lemkul <jalemkul at vt.edu>
> ha
> > scritto:
> >
> >>
> >>
> >> On 8/20/15 3:17 AM, Simone Bolognini wrote:
> >>> Hi everyone,
> >>> I have a .pdb file of the WW domain of human FIP35 protein extracted
> from
> >>> an MD calculation obtained with AMBER ff99SB-ILDN and solvent type
> tip3.
> >>> Now I need to obtain the topology out of it, but the .pdb contains a
> >>> residue, namely HSD, which is not present in the Amber residue
> database.
> >> I
> >>> looked at the source files and found out that CHARMM has it. In
> >> particular,
> >>> this is what you can find in the CHARMM database:
> >>>
> >>> [ HSD ]
> >>>    [ atoms ]
> >>> N NH1 -0.47 0
> >>> HN H 0.31 1
> >>> CA CT1 0.07 2
> >>> HA HB 0.09 3
> >>> CB CT2 -0.09 4
> >>> HB1 HA 0.09 5
> >>> HB2 HA 0.09 6
> >>> ND1 NR1 -0.36 7
> >>> HD1 H 0.32 8
> >>> CG CPH1 -0.05 9
> >>> CE1 CPH2 0.25 10
> >>> HE1 HR1 0.13 11
> >>> NE2 NR2 -0.70 12
> >>> CD2 CPH1 0.22 13
> >>> HD2 HR3 0.10 14
> >>> C C 0.51 15
> >>> O O -0.51 16
> >>>    [ bonds ]
> >>> CB CA
> >>> CG CB
> >>> ND1 CG
> >>> CE1 ND1
> >>> NE2 CD2
> >>> N HN
> >>> N CA
> >>> C CA
> >>> C +N
> >>> CA HA
> >>> CB HB1
> >>> CB HB2
> >>> ND1 HD1
> >>> CD2 HD2
> >>> CE1 HE1
> >>> O C
> >>> CG CD2
> >>> CE1 NE2
> >>>    [ impropers ]
> >>> ND1 CG CE1 HD1
> >>> CD2 CG NE2 HD2
> >>> CE1 ND1 NE2 HE1
> >>> ND1 CE1 CG HD1
> >>> CD2 NE2 CG HD2
> >>> CE1 NE2 ND1 HE1
> >>> N -C CA HN
> >>> C CA +N O
> >>>    [ cmap ]
> >>> -C N CA C +N
> >>>
> >>> Is there any possible way in which I can "copy and paste" this in the
> >> Amber
> >>> database and hope it will work correctly? Thank you very much!!!
> >>>
> >>
> >> No, you can't copy and paste, because then you're mixing force fields
> and
> >> that
> >> is bad practice.  HSD is just delta-protonated HIS, which is already in
> >> AMBER.
> >> It's just called HID, so rename your coordinate files appropriately and
> >> you can
> >> generate the topology.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 629
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==================================================
> >> --
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>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
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