[gmx-users] HB3 ATOM

[Mahdi Sobati Nezhad]

please excuse me sir


On Mon, 3 Sep 2018 22:59 Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> On 9/3/18 2:28 PM, Mahdi Sobati Nezhad wrote:
> > how can I build hydrogens own, after -ignh command?!
>
> Please re-read what I just said.
>
> -Justin
>
> > On Mon, 3 Sep 2018 22:55 Justin Lemkul, <jalemkul at vt.edu> wrote:
> >
> >>
> >> On 9/3/18 2:24 PM, Mahdi Sobati Nezhad wrote:
> >>> Yes. Now my problem is HG in residue CYS that I don't know rename to
> >> what!!!
> >>
> >> Either the names in the PDB file need to be made consistent with what is
> >> in the .rtp file, or you should use -ignh to have pdb2gmx ignore all
> >> input H atoms and build its own, all of which will be properly named.
> >>
> >> -Justin
> >>
> >>> On Mon, 3 Sep 2018 22:49 Justin Lemkul, <jalemkul at vt.edu> wrote:
> >>>
> >>>> On 9/3/18 6:27 AM, Mahdi Sobati Nezhad wrote:
> >>>>> Hi
> >>>>> my pdb file named HB2 and HB3 but .rtp file in  my force field named
> >>>> HB1and
> >>>>> HB2. and so on error "atom HB3 in residue xxx was not found in rtp
> >> entry"
> >>>>> can I rename HB2 to HB1 and HB3 to HB2 ?
> >>>>> or any idea?!
> >>>> Have you tried it?
> >>>>
> >>>> -Justin
> >>>>
> >>>> --
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> >>>> Justin A. Lemkul, Ph.D.
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> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Virginia Tech Department of Biochemistry
> >>
> >> 303 Engel Hall
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
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