[gmx-users] Opening PDB files in GROMACS on Windows using Cygwin
Neena Susan Eappen
neena.susaneappen at mail.utoronto.ca
Sat Nov 3 03:16:17 CET 2018
Thank you Benson Muite and Bratin Kumar for replying. I am using version 5.1.1. Thanks Bratin for pointing that out, now it works when the file was transferred to the working directory!
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of gromacs.org_gmx-users-request at maillist.sys.kth.se <gromacs.org_gmx-users-request at maillist.sys.kth.se>
Sent: Friday, November 2, 2018 3:51 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: gromacs.org_gmx-users Digest, Vol 175, Issue 9
Send gromacs.org_gmx-users mailing list submissions to
gromacs.org_gmx-users at maillist.sys.kth.se
To subscribe or unsubscribe via the World Wide Web, visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
or, via email, send a message with subject or body 'help' to
gromacs.org_gmx-users-request at maillist.sys.kth.se
You can reach the person managing the list at
gromacs.org_gmx-users-owner at maillist.sys.kth.se
When replying, please edit your Subject line so it is more specific
than "Re: Contents of gromacs.org_gmx-users digest..."
Today's Topics:
1. Re: Gmx distance (rose rahmani)
2. Opening PDB files in GROMACS on Windows using Cygwin
(Neena Susan Eappen)
3. Re: Opening PDB files in GROMACS on Windows using Cygwin
(Benson Muite)
4. Re: Opening PDB files in GROMACS on Windows using Cygwin
(Bratin Kumar Das)
----------------------------------------------------------------------
Message: 1
Date: Fri, 2 Nov 2018 19:06:36 +0330
From: rose rahmani <rose.rhmn93 at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Gmx distance
Message-ID:
<CAO6==5TPaj+HE1JZQKXQSCkZun4oQJbxvpBntoeWup0XCvKeUQ at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
but this is output of -oall. its not a single value?!
gmx distance -f md2.xtc -oall dist.xvg -n index.ndx
# gmx distance is part of G R O M A C S:
#
#
??<8d><9a><9a><91>???<9a><9b>???<8d><9e><91><98><9a>???<9e><98><9a><91><8b><9e>???<85><8a><8d><9a>???<86><9e><91>???<94><86><9d><99a>8a><<
#
@ title "Distance"
@ xaxis label "Time (ps)"
@ yaxis label "Distance (nm)"
@TYPE xy
1.000 0.229 0.229 0.446 0.582 0.446 0.229 0.446
0.583 0.447 0.229 0.447 0.227 0.228 0.229 0.446
0.582 0.446 0.228 0.446 0.583 0.447 0.228 0.447
0.227 0.227 0.228 0.446 0.582 0.446 0.227 0.446
0.583 0.447 0.227 0.447 0.227 0.228 0.229 0.446
0.582 0.446 0.228 0.446 0.583 0.447 0.228 0.447
0.227 0.228 0.229 0.446 0.582 0.446 0.228 0.446
0.583 0.447 0.228 0.447 0.227 0.229 0.229 0.446
0.582 0.446 0.229 0.446 0.583 0.447 0.229 0.447
0.227 0.229 0.229 0.446 0.582 0.446 0.229 0.446
0.583 0.447 0.229 0.447 0.227 0.228 0.229 0.446
0.582 0.446 0.228 0.446 0.583 0.447 0.228 0.447
0.227 0.228 0.229 0.446 0.582 0.446 0.228 0.446
0.583 0.447 0.228 0.447 0.227 0.227 0.228 0.446
0.582 0.446 0.227 0.446 0.583 0.447 0.227 0.447
0.227 0.228 0.229 0.446 0.582 0.446 0.228 0.446
0.583 0.447 0.228 0.4
.
.
.
and this is -o of g_dist;
g_dist -f md2.xtc -s md2.tpr -n index -o all.xvg
#
# g_dist is part of G R O M A C S:
#
# GRowing Old MAkes el Chrono Sweat
#
@ title "Distance"
@ xaxis label "Time (ps)"
@ yaxis label "Distance (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
0.0000000 0.2176011 -0.0120678 -0.0465498 0.2122209
1.0000000 0.2124534 -0.0301750 -0.0463870 0.2051198
2.0000000 0.1923753 -0.0158403 -0.0510135 0.1848106
3.0000000 0.1885315 -0.0107298 -0.0488160 0.1817856
4.0000000 0.2044982 -0.0052650 -0.0490329 0.1984630
5.0000000 0.2033602 -0.0002742 -0.0429537 0.1987720
6.0000000 0.2050487 0.0013833 -0.0444658 0.2001646
7.0000000 0.2002475 0.0041072 -0.0415003 0.1958568
8.0000000 0.2006473 0.0033450 -0.0511889 0.1939790
9.0000000 0.2032918 -0.0000119 -0.0330052 0.2005947
10.0000000 0.2255659 0.0003929 -0.0415857 0.2216990
11.0000000 0.2243811 0.0118313 -0.0344751 0.2214010
12.0000000 0.2347855 0.0078275 -0.0383532 0.2314994
13.0000000 0.2371541 0.0081918 -0.0388267 0.2338107
.
.
.
On Thu, Nov 1, 2018 at 11:39 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 11/1/18 2:25 PM, rose rahmani wrote:
> > I don't know how? I mean x,y,z(s1, s2,s3) in dist.xvg can easily be
> > multiplied by (-), but how should i modify second column,i don't know how
> > s0 is calculated by g_distance to modify it??
>
> The output of -oall is a single value, the actual distance, which I
> assume is what you are talking about in your previous message. You can
> parse that column in any scripting language you like and
>
> [ pseudocode, not functional ]
> if (value < 0)
> {
> value *= -1
> }
>
> -Justin
> > On Wed, 31 Oct 2018, 19:38 Justin Lemkul, <jalemkul at vt.edu> wrote:
> >
> >>
> >> On 10/31/18 12:06 PM, rose rahmani wrote:
> >>> Hi,
> >>>
> >>> I want to calculate distances between fixed tube in the middle of the
> box
> >>> and amino acids(all are same type)around it. But gmx distance gives me
> >> the
> >>> relative distance i mean AA can be front or back( can be 0.5 or -0.5
> from
> >>> tube) of tube but still |-0.5|=0.5 nm far from it. How can i have the
> >>> absolute value of distances?
> >>> Would you please help me?
> >> Write a simple post-processing script that multiplies any negative value
> >> by -1.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> 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
> >>
> >> ==================================================
> >>
> >> --
> >> 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-request at gromacs.org.
> >>
>
> --
> ==================================================
>
> 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
>
> ==================================================
>
> --
> 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-request at gromacs.org.
------------------------------
Message: 2
Date: Fri, 2 Nov 2018 15:45:44 +0000
From: Neena Susan Eappen <neena.susaneappen at mail.utoronto.ca>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] Opening PDB files in GROMACS on Windows using
Cygwin
Message-ID:
<YQBPR0101MB2097A16098099044AF4790F7CDCF0 at YQBPR0101MB2097.CANPRD01.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="iso-8859-1"
Hello GROMACS users,
I am a first time user of GROMACS. According to this excellent tutorial (http://www.mdtutorials.com/gmx/lysozyme/01_pdb2gmx.html), I downloaded the PDB file for lyzozyme, then removed water molecules, typed in the following command on CygwinShell (with GROMACS activated).
$ gmx pdb2gmx -f 1AKI_clean.pdb -o 1AKI_processed.gro -water spce
However, I get an error saying:
In command line option -f, file 1AKI_clean.pdb does not exit or is not accessible.
Please advice where am I going wrong. Any insight would be appreciated.
Many thanks,
Neena Eappen
Graduate Student
Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T
------------------------------
Message: 3
Date: Fri, 2 Nov 2018 15:48:25 +0000
From: Benson Muite <benson.muite at ut.ee>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] Opening PDB files in GROMACS on Windows using
Cygwin
Message-ID: <4620f59c-af79-9813-74e8-078766541f5d at ut.ee>
Content-Type: text/plain; charset="utf-8"
What version of GROMACS are you using?
On 11/2/18 5:45 PM, Neena Susan Eappen wrote:
> Hello GROMACS users,
>
>
> I am a first time user of GROMACS. According to this excellent tutorial (http://www.mdtutorials.com/gmx/lysozyme/01_pdb2gmx.html), I downloaded the PDB file for lyzozyme, then removed water molecules, typed in the following command on CygwinShell (with GROMACS activated).
>
> $ gmx pdb2gmx -f 1AKI_clean.pdb -o 1AKI_processed.gro -water spce
>
> However, I get an error saying:
>
> In command line option -f, file 1AKI_clean.pdb does not exit or is not accessible.
>
> Please advice where am I going wrong. Any insight would be appreciated.
>
> Many thanks,
>
> Neena Eappen
> Graduate Student
> Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T
------------------------------
Message: 4
Date: Fri, 2 Nov 2018 21:21:26 +0530
From: Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Opening PDB files in GROMACS on Windows using
Cygwin
Message-ID:
<CAM7TW5t_k8b_bU4P1fiSnJ2B75=E6Ge7pu4PbPTwXAoF+xmK5Q at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
What ever version you use if the file is not present in your working
directory
..it will give the same error
On Fri, Nov 2, 2018, 9:18 PM Benson Muite <benson.muite at ut.ee> wrote:
> What version of GROMACS are you using?
>
> On 11/2/18 5:45 PM, Neena Susan Eappen wrote:
> > Hello GROMACS users,
> >
> >
> > I am a first time user of GROMACS. According to this excellent tutorial (
> http://www.mdtutorials.com/gmx/lysozyme/01_pdb2gmx.html), I downloaded
> the PDB file for lyzozyme, then removed water molecules, typed in the
> following command on CygwinShell (with GROMACS activated).
> >
> > $ gmx pdb2gmx -f 1AKI_clean.pdb -o 1AKI_processed.gro -water spce
> >
> > However, I get an error saying:
> >
> > In command line option -f, file 1AKI_clean.pdb does not exit or is not
> accessible.
> >
> > Please advice where am I going wrong. Any insight would be appreciated.
> >
> > Many thanks,
> >
> > Neena Eappen
> > Graduate Student
> > Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T
> --
> 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-request at 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-request at gromacs.org.
End of gromacs.org_gmx-users Digest, Vol 175, Issue 9
*****************************************************
More information about the gromacs.org_gmx-users
mailing list