From owner-chemistry@ccl.net Sun Oct 14 15:37:01 2007 From: "Marcin Krol mykrol{}cyf-kr.edu.pl" To: CCL Subject: CCL: AminoAcid Rotamer Analysis Message-Id: <-35379-071013184245-14908-y0BoHQIMTg6YJrjtnADDhQ,,server.ccl.net> X-Original-From: Marcin Krol Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Sat, 13 Oct 2007 23:40:56 +0200 (METDST) MIME-Version: 1.0 Sent to CCL by: Marcin Krol [mykrol#,#cyf-kr.edu.pl] Hi Cesar, Try g_chi from the Gromacs suite (www.gromacs.org). It's free but I'm afraid you'll have to install the whole package. Alternatively, you can do the time series of any dihedral in CHARMM using correl command, but I think you'll have to define each dihedral separately and it won't give you directly rotamer count (eg. you'll have to check which rotamer states were sampled by looking at dihedral values). Hope this helps Marcin Dr Marcin Krol Biomolecular Modelling Laboratory Cancer Research UK e-mail: marcin.krol%cancer.org.uk AND Department of Bioinformatics Collegium Medicum Jagiellonian University e-mail: mykrol%cyf-kr.edu.pl On Fri, 12 Oct 2007, Cesar Millan pachequin:-:gmail.com wrote: > > Sent to CCL by: "Cesar Millan" [pachequin^^^gmail.com] Hi everyone! I > have a couple of protein dynamics made by CHARMM (dcd format) and I want > to do a dihedral analysis of the aminoacids on my protein. I knew a > program called Dials and Windows that could this kind of analysis, but > it only runs on SGI machines. > > Does anyone knows any free software that could realize this kind of > analysis on linux machines? > > Any help would be appreciate. > > Best Regards. > > Cesar.> > > From owner-chemistry@ccl.net Sun Oct 14 21:46:01 2007 From: "Cesar Millan pachequin^gmail.com" To: CCL Subject: CCL: AminoAcid Rotamer Analysis Message-Id: <-35380-071014165444-12667-Z8JgaTTjLqEwfqz3tPA8Mw-$-server.ccl.net> X-Original-From: "Cesar Millan" Content-Type: multipart/alternative; boundary="----=_Part_14812_25497389.1192393524601" Date: Sun, 14 Oct 2007 15:25:24 -0500 MIME-Version: 1.0 Sent to CCL by: "Cesar Millan" [pachequin_+_gmail.com] ------=_Part_14812_25497389.1192393524601 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Marcin, I think that g_chi could be simpler but g_chi reads dcd trajectory generated by charmm? or I have to change it to xtc? beside the xtc i need other archives or am I wrong? thanks for your help. On 10/13/07, Marcin Krol mykrol{}cyf-kr.edu.pl wrote: > > > Sent to CCL by: Marcin Krol [mykrol#,#cyf-kr.edu.pl] > > Hi Cesar, > > Try g_chi from the Gromacs suite (www.gromacs.org). It's free but I'm > afraid you'll have to install the whole package. > Alternatively, you can do the time series of any dihedral in CHARMM > using correl command, but I think you'll have to define each dihedral > separately and it won't give you directly rotamer count (eg. you'll have > to check which rotamer states were sampled by looking at dihedral values)= . > > Hope this helps > Marcin > > Dr Marcin Krol > Biomolecular Modelling Laboratory > Cancer Research UK > e-mail: marcin.krol]![cancer.org.uk > AND > Department of Bioinformatics > Collegium Medicum Jagiellonian University > e-mail: mykrol]![cyf-kr.edu.pl > > > On Fri, 12 Oct 2007, Cesar Millan pachequin:-:gmail.com wrote: > > > > > Sent to CCL by: "Cesar Millan" [pachequin^^^gmail.com] Hi everyone! I > > have a couple of protein dynamics made by CHARMM (dcd format) and I wan= t > > to do a dihedral analysis of the aminoacids on my protein. I knew a > > program called Dials and Windows that could this kind of analysis, but > > it only runs on SGI machines. > > > > Does anyone knows any free software that could realize this kind of > > analysis on linux machines? > > > > Any help would be appreciate. > > > > Best Regards. > > > > Cesar.> > > > > > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > --=20 ########### "There is no form of prose more difficult to understand and more tedious to read than the average scientific paper." -- Francis Crick, "The Astonishing Hypothesis" ########### C=E9sar Mill=E1n Pacheco Facultad de Ciencias Universidad Autonoma del Estado de Morelos Tel: 777 3297020 Fax: 777 3207040 email: cmp+/-servm.fc.uaem.mx pachequin+/-gmail.com ------=_Part_14812_25497389.1192393524601 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Marcin, I think that g_chi could be simpler but g_chi reads dcd trajecto= ry generated by charmm? or I have to change it to xtc? beside the xtc i nee= d other archives or am I wrong?

thanks for your help.

On 10/13/07, Marc= in Krol mykrol{}cyf-kr.edu.pl <owner-chemistry+/-ccl.net> wrot= e:

Sent to CCL b= y: Marcin Krol [mykrol#,#cyf-kr.edu.pl]
Hi Cesar,

Try g_chi from the Gromacs suite (www.gromacs.org). It's free but I'm
afraid you= 9;ll have to install the whole package.
Alternatively, you can do the ti= me series of any dihedral in CHARMM
using correl command, but I think you'll have to define each dihedr= al
separately and it won't give you directly rotamer count (eg. you&= #39;ll have
to check which rotamer states were sampled by looking at dih= edral values).

Hope this helps
Marcin

Dr Marcin Krol
Biomolecular Mod= elling Laboratory
Cancer Research UK
e-mail: marcin.krol]![cancer.org.uk
AND
Department of Bioinforma= tics
Collegium Medicum Jagiellonian University
e-mail: mykrol]![cyf-kr.edu.pl


On Fri, 12 Oct 2007,= Cesar Millan pachequin:-:gmail.com wrote:=

>
> Sent to CCL by: "Cesar Millan" [pachequin^^^gmail.com] Hi everyone! I
> have a coupl= e of protein dynamics made by CHARMM (dcd format) and I want
> to do = a dihedral analysis of the aminoacids on my protein. I knew a
> program called Dials and Windows that could this kind of analysis,= but
> it only runs on SGI machines.
>
> Does anyone know= s any free software that could realize this kind of
> analysis on lin= ux machines?
>
> Any help would be appreciate.
>
> Best Regards= .
>
> Cesar.>
>
>



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--
###########
"T= here is no form of prose more difficult to understand and more tedious to r= ead
than the average scientific paper."
    &n= bsp;            = ;        -- Francis Crick, "The Ast= onishing Hypothesis"  

###########

C=E9sar Mil= l=E1n Pacheco
Facultad de Ciencias
Universidad Autonoma del Estado de= Morelos
Tel: 777 3297020
Fax: 777 3207040
email: cmp+/-servm.fc.uaem.mx
     &= nbsp;    pachequ= in+/-gmail.com ------=_Part_14812_25497389.1192393524601--