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

[Simone Bolognini]

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.

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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