Re: [gmx-users] Analaysis

[‪Mohammad Roostaie‬ ‪]

Hi Amir,
I used these commands for installing:
sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 -O 
/usr/local/bin/dssp

sudo add-apt-repository ppa:sfleischmann/tcbsys

sudo apt-get update

sudo apt-get install dssp


and these for running:
do_dssp -f md.xtc -s md.tpr -o dsso.xpm -sc dssp.xvg

xpm2ps  -f dssp.xpm -o dssp.eps -di ps.m2p

ps2pdf dssp.eps dssp.pdf


Best,Mohammad
  From: Amir Zeb <zebami...@gmail.com>
 To: gmx-us...@gromacs.org 
 Sent: Monday, 12 December 2016, 6:05:23
 Subject: Re: [gmx-users] Analaysis
   
hello mohammad

can you please let me know how to install do_dssp on my gromacs 5.0.6
we have downloaded the package but we could not install
please help

thanks

On Dec 11, 2016 11:45 PM, "Justin Lemkul" <jalem...@vt.edu> wrote:

>
>
> On 12/11/16 1:01 AM, ‪Mohammad Roostaie‬ ‪ wrote:
>
>>
>>
>>
>> Hi Gromacs users, I want to obtain the percentage of helicity of a peptide
>> with respect to time after the simulation, how can I get it? I used the
>> "gmx
>> helix" and "gmx do_dssp" commands, but I could not get it. In addition, I
>>
>
> The last line in scount.xvg from gmx do_dssp gives you this.
>
> want to get the number of clusters and contact area of two particles with
>> respect to time, and I used "gmx clustsize" and "gmx mindist" commands,
>> but I
>> still cannot get these factors. can you please help me figure this out?
>> Thank
>>
>
> gmx clustsize has output options for number of clusters, cluster size,
> distribution, etc.
>
> If you want contact area, use gmx sasa with appropriate index groups.
>
> -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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

   
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Analaysis

[‪Mohammad Roostaie‬ ‪]

Thank you very much Justin
Best,Mohammad

  From: Justin Lemkul <jalem...@vt.edu>
 To: gmx-us...@gromacs.org 
 Sent: Sunday, 11 December 2016, 18:15:01
 Subject: Re: [gmx-users] Analaysis
   


On 12/11/16 1:01 AM, ‪Mohammad Roostaie‬ ‪ wrote:
>
>
>
> Hi Gromacs users, I want to obtain the percentage of helicity of a peptide
> with respect to time after the simulation, how can I get it? I used the "gmx
> helix" and "gmx do_dssp" commands, but I could not get it. In addition, I

The last line in scount.xvg from gmx do_dssp gives you this.

> want to get the number of clusters and contact area of two particles with
> respect to time, and I used "gmx clustsize" and "gmx mindist" commands, but I
> still cannot get these factors. can you please help me figure this out? Thank

gmx clustsize has output options for number of clusters, cluster size, 
distribution, etc.

If you want contact area, use gmx sasa with appropriate index groups.

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

   
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Analaysis

[Amir Zeb]

hello mohammad

can you please let me know how to install do_dssp on my gromacs 5.0.6
we have downloaded the package but we could not install
please help

thanks

On Dec 11, 2016 11:45 PM, "Justin Lemkul"  wrote:

>
>
> On 12/11/16 1:01 AM, ‪Mohammad Roostaie‬ ‪ wrote:
>
>>
>>
>>
>> Hi Gromacs users, I want to obtain the percentage of helicity of a peptide
>> with respect to time after the simulation, how can I get it? I used the
>> "gmx
>> helix" and "gmx do_dssp" commands, but I could not get it. In addition, I
>>
>
> The last line in scount.xvg from gmx do_dssp gives you this.
>
> want to get the number of clusters and contact area of two particles with
>> respect to time, and I used "gmx clustsize" and "gmx mindist" commands,
>> but I
>> still cannot get these factors. can you please help me figure this out?
>> Thank
>>
>
> gmx clustsize has output options for number of clusters, cluster size,
> distribution, etc.
>
> If you want contact area, use gmx sasa with appropriate index groups.
>
> -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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Analaysis

[Justin Lemkul]

On 12/11/16 1:01 AM, ‪Mohammad Roostaie‬ ‪ wrote:




Hi Gromacs users, I want to obtain the percentage of helicity of a peptide
with respect to time after the simulation, how can I get it? I used the "gmx
helix" and "gmx do_dssp" commands, but I could not get it. In addition, I


The last line in scount.xvg from gmx do_dssp gives you this.


want to get the number of clusters and contact area of two particles with
respect to time, and I used "gmx clustsize" and "gmx mindist" commands, but I
still cannot get these factors. can you please help me figure this out? Thank


gmx clustsize has output options for number of clusters, cluster size, 
distribution, etc.


If you want contact area, use gmx sasa with appropriate index groups.

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Analaysis

[‪Mohammad Roostaie‬ ‪]

   
Hi Gromacs users,
I want to obtain the percentage of helicity of a peptide with respect to time 
after the simulation, how can I get it? I used the "gmx helix" and "gmx 
do_dssp" commands, but I could not get it.
In addition, I want to get the number of clusters and contact area of two 
particles with respect to time, and I used "gmx clustsize" and "gmx mindist" 
commands, but I still cannot get these factors. can you please help me figure 
this out?
Thank you,Mohammad

   
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.