[gmx-users] DSSP with custom residues

[Justin Lemkul]

On 4/26/16 1:10 PM, leila salimi wrote:
> 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?
>

Well, your x-axis will be 800x longer than your y-axis by default, so do the 
math (simple proportions!) to generate a suitably sized rectangular plot.

-Justin

>
> 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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
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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

==================================================