[gmx-users] DSSP with custom residues

[leila salimi]

Thanks very much.

I have one problem, I am trying to use xpm2ps to plot the secondary
structure!
I used the m2p file from this link:

http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water_(Pt._2)

My problem is that the plot is not correct. I tried different xbox and ybox
but it is not working and I got confused!

I have 10 residues and 400 ns time simulations ( 80001 frames).
For this file how can I  fix the xbox and ybox parameters?


Thanks in advance,

On Tue, Apr 26, 2016 at 3:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/26/16 9:10 AM, leila salimi wrote:
>
>> Hi Justin,
>>
>> I am also busy by DSSP analysis. I am interested to know what the
>> difference between do_dssp and dssp is?
>>
>>
> dssp is a binary that actually carries out the DSSP analysis; it is not a
> GROMACS program but is downloaded from an external source.  do_dssp is a
> GROMACS module that is just a wrapper - it runs through a trajectory, pulls
> out the coordinates to a temporary file (those ddXXXX files that show up),
> passes those coordinates to dssp, and records the output.  GROMACS doesn't
> do secondary structure calculations natively, instead relying on dssp.
>
> -Justin
>
>
> Regards,
>> Leila
>>
>> On Tue, Apr 26, 2016 at 3:00 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 4/26/16 8:57 AM, Stephanie Jephthah wrote:
>>>
>>> Hi!
>>>>
>>>> I'm simulating a protein conjugate and thus uses custom residues. Is
>>>> there
>>>> any way to make the dssp program aware of the custom residues (and does
>>>> it
>>>> make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm
>>>> assuming that the problem is not with do_dssp but with dssp, but please
>>>> correct me if I'm wrong.
>>>>
>>>>
>>>> If you've got custom residues as integral parts of the protein, they
>>> need
>>> to be defined as such in residuetypes.dat, or otherwise defined in a
>>> suitable custom index group.  Presumably you have to have done one or the
>>> other before running the simulation.  If the custom residues have normal
>>> amino acid backbone features, doing DSSP analysis makes sense.  If
>>> something is failing, run dssp directly, not via do_dssp, to determine if
>>> the failure is within dssp or do_dssp.
>>>
>>> -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
>
> ==================================================
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> Gromacs Users mailing list
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