On 10/30/13 2:34 PM, Hari Pandey wrote:
Dear Gromacs users,
Please somebody help .
editconf computs the incorrect value of "mass of input". I tried to resolve
this problem but failed. Previously I was doing AOt but now I just found that the
molecule OS1 =O2L showing error . Here I posted m
Hi Jonathan,
I suspect the dash is not of the right kind. Did you by chance copy/paste
the command? Did you try typing it?
Cheers,
Tsjerk
On Sat, Jul 13, 2013 at 12:03 AM, Jonathan Saboury wrote:
> I am following "Tutorial 1" from
> https://extras.csc.fi/chem/courses/gmx2007/tutorial1/index.
On 4/1/13 8:55 PM, Juliette N. wrote:
Hi Justin
I tried several residue names, 1Ethylene, 1Eth but editconf says:
Program editconf, VERSION 4.5.4
Source code file: pdbio.c, line: 446
Software inconsistency error:
Trying to deduce atomnumbers when no pdb information is present
For more infor
Hi Justin
I tried several residue names, 1Ethylene, 1Eth but editconf says:
Program editconf, VERSION 4.5.4
Source code file: pdbio.c, line: 446
Software inconsistency error:
Trying to deduce atomnumbers when no pdb information is present
For more information and tips for troubleshooting, pleas
On 4/1/13 7:22 PM, Juliette N. wrote:
Hi all,
I am trying to produce gro file from PDB file using editconf.
Here is the pdb file
HETATM1 C 0.672 -0.000
0.000 C
HETATM2 C -0.672 -0.000
0.000 C
HETATM
Thank Erik and Dallas so much !
I got it :-)
On Fri, Feb 22, 2013 at 4:53 AM, Dallas Warren wrote:
> If you have a particle at 1.000 1.000 1.000
>
> If use editconf -translate 0 1 -1
>
> Then that particle will be moved to 1.000 2.000 0.000
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Discovery Bi
If you have a particle at 1.000 1.000 1.000
If use editconf -translate 0 1 -1
Then that particle will be moved to 1.000 2.000 0.000
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war..
Hi,
What difference does it make? All coordinates are translated by a
fixed vector. There is no need for a reference point.
Best,
Erik
On Feb 21, 2013, at 3:31 PM, Kieu Thu Nguyen wrote:
Dear all,
I am not clear about the option -translate following editconf tool.
Whether the coordinates
On 12/31/12 5:50 PM, Xu Dong Huang wrote:
Dear Justin,
I'm pretty sure my .gro file is valid, here is a direct copy and paste of the
format of my .gro in the beginning:
star polymer
201
1starO41 0.000 0.000 0.000
1star O12 0.430 0.000 0.000
1s
Ok I sent it.
Let me know if you did not receive them.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Dec 31, 2012, at 5:54 PM, Justin Lemkul wrote:
>
>
> On 12/31/12 5:50 PM, Xu Dong Huang wrote:
>> Dear Justin,
>>
>> I'm prett
On 12/31/12 5:50 PM, Xu Dong Huang wrote:
Dear Justin,
I'm pretty sure my .gro file is valid, here is a direct copy and paste of the
format of my .gro in the beginning:
star polymer
201
1starO41 0.000 0.000 0.000
1star O12 0.430 0.000 0.000
1s
Dear Justin,
I'm pretty sure my .gro file is valid, here is a direct copy and paste of the
format of my .gro in the beginning:
star polymer
201
1starO41 0.000 0.000 0.000
1starO12 0.430 0.000 0.000
1starO13 0.860 0.000 0.000
On 12/31/12 5:40 PM, Xu Dong Huang wrote:
Dear Justin,
(here is the picture of the molecule after editconf, note the negative x and
negative y axis is missing the rest of the beads that is suppose to be like the
positive x and positive y)
http://i1284.photobucket.com/albums/a571/X_huang1/Scr
Dear Justin,
(here is the picture of the molecule after editconf, note the negative x and
negative y axis is missing the rest of the beads that is suppose to be like the
positive x and positive y)
http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2012-12-31at53618PM_zpse5f421f1.png
*
On 12/31/12 4:53 PM, Xu Dong Huang wrote:
Dear advanced gromacs users,
I have created an arbitrary molecule .gro file containing coordinates of my
martini-beads. basically, there are 50 beads sitting on each axis of (x,y, -x
and -y) forming like a cross. (Each bead with distance 0.43). Howev
On 6/29/12 4:48 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I want to put my protein in a box with the command:
editconf -f 3m71.gro -o 3m71_box.gro -c -bt dodecahedron -d 1.0 2>>logErr
1>>logOut
and add solvent afterwards with:
genbox -cp 3m71_box.gro -cs spc216.gr
Thank you for your clarification.
On Sat, May 12, 2012 at 2:51 AM, Justin A. Lemkul wrote:
>
>
> On 5/11/12 7:40 PM, Nitin Agrawal wrote:
>
>> Hi,
>>
>> Can anyone please tell me what is the difference between the commands
>> editconf
>> and g_editconf? If there is no difference then why do some
On 5/11/12 7:40 PM, Nitin Agrawal wrote:
Hi,
Can anyone please tell me what is the difference between the commands editconf
and g_editconf? If there is no difference then why do some systems recognize
g_editconf but not editconf?
There is no difference. g_editconf is just editconf but with
mohammad agha wrote:
Dear Prof.
May I know the best quantity for -d option in editconf program? for
example for a cubic box consists of 7 water molecules and 500
surfactant molecules with 22 , 022 , 22 box dimensions in x , y and z?
If you've got a box built, what's the need for -d?
Hi Mustafa,
Check the section on periodic boundary conditions in the manual. Also
be sure to use 'show cell' in Pymol to display the triclinic unit
cell. That will show you the differences. Besides that, do a direct
comparison of the lines encoding the boxes; either the last line of a
.gro fil, or
OMACS users
Subject: Re: [gmx-users] editconf
On 19/10/2010 12:22 PM, Payman Pirzadeh wrote:
> After rotation, wouldn't a minimization with very very small steps solve
the
> problem?
Only if the solute surface was very close to being symmetric about the
rotation axis. Since th
ity to try.
Mark
Paymon
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Mark Abraham
Sent: October 18, 2010 7:14 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] editconf
On 19/10/2010 8:11 AM, Paymon Pirz
th solvent. Far more reliable.
-Justin
Paymon
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Mark Abraham
Sent: October 18, 2010 7:14 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] editconf
On 19/10/20
users
Subject: Re: [gmx-users] editconf
On 19/10/2010 8:11 AM, Paymon Pirzadeh wrote:
> Hello,
> I am trying to rotate my protein in my simulation box (solvent molecules
> are there as well). I issue the following command:
> editconf_d_mpi -f AFPIII_Ih0001_54_26_em.gro -n protein.ndx -rot
On 19/10/2010 8:11 AM, Paymon Pirzadeh wrote:
Hello,
I am trying to rotate my protein in my simulation box (solvent molecules
are there as well). I issue the following command:
editconf_d_mpi -f AFPIII_Ih0001_54_26_em.gro -n protein.ndx -rotate 15
180 0 -o AFPIII_Ih0001_54_26_rotated.gro -box
Hello,
I am trying to rotate my protein in my simulation box (solvent molecules
are there as well). I issue the following command:
editconf_d_mpi -f AFPIII_Ih0001_54_26_em.gro -n protein.ndx -rotate 15
180 0 -o AFPIII_Ih0001_54_26_rotated.gro -box 5.40022 6.23564 20.59328
I select my group (prote
- Original Message -
From: abdullah ahmed
Date: Saturday, August 14, 2010 1:05
Subject: [gmx-users] editconf
To: gmx
---
|
>
Hello,
>
> I'd like to ask a question about the conversion of the results of
> minimization to pdb for
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Fri, Aug 13, 2010 at 8:08 AM, Justin A. Lemkul wrote:
>
>
> abdullah ahmed wrote:
>
>> Hello,
>>
>> I'd like to ask a question about the conversion of the results of
>> minimization to pdb format. Here is what I do:
>>
>> 1. Apply pdb2gmx to the p
abdullah ahmed wrote:
Hello,
I'd like to ask a question about the conversion of the results of
minimization to pdb format. Here is what I do:
1. Apply pdb2gmx to the pdb file to convert it to .gro and .top
(pdb2gmx -f -p -o)
2. Run editconf to define the box (editconf -d 1)
thanks. things are getting clearer and life's going a little easier, now.
Justin A. Lemkul schrieb:
>
>
> dur...@zib.de wrote:
>> hi there,
>>
>> it's my first steps with gromacs and i can't get rid of the following
>> problem:
>>
>> i set up my box with
>>
>> editconf -bt dodecahedron -f complex
dur...@zib.de wrote:
hi there,
it's my first steps with gromacs and i can't get rid of the following
problem:
i set up my box with
editconf -bt dodecahedron -f complex.pdb -o complex.pdb -c -d 0.9
and fill it up with water like
genbox -cp complex.pdb -cs ffamber_tip3p.gro -o outfile.pdb -p
Carsten Kutzner wrote:
On Dec 21, 2009, at 5:26 PM,
wrote:
Dear Users,
Re Introductory tutorial;
Trying to run the following:
editconf -f out.gro -o fws_ctr.gro -center x/2 y/2 z/2
You have to give real coordinates for the center, not
in terms of x, y, z. The coordinates are given e.
On Dec 21, 2009, at 5:26 PM,
wrote:
> Dear Users,
>
>
>
> Re Introductory tutorial;
>
>
>
> Trying to run the following:
>
> editconf -f out.gro -o fws_ctr.gro -center x/2 y/2 z/2
You have to give real coordinates for the center, not
in terms of x, y, z. The coordinates are given e.g. a
Sent: Friday, September 18, 2009 7:21 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] editconf and g_rmsdist
Hi Soren,
> Why I am seeing this difference? Is it due to round-off's after the
> transformation to center the molecule in the box? Or am I using g_rmsdist
>
Hi Soren,
> Why I am seeing this difference? Is it due to round-off’s after the
> transformation to center the molecule in the box? Or am I using g_rmsdist
> wrongly?
It's a bit weird indeed. You might be right that it's due to round-off
errors. You can try to copy the original gro file and repl
Homa Azizian wrote:
Hi
These 2 warning appeared after I did editconf for Drug-Protein Complex.
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
WARNING: vdwradii will be determined based on residue and atom nam
Thank you very much.
Trjconv works fine.
Marian
On Mon, Mar 9, 2009 at 1:10 PM, Justin A. Lemkul wrote:
>
>
> Mark Abraham wrote:
>
>> - Original Message -
>> From: Nuno Azoia
>> Date: Monday, March 9, 2009 21:52
>> Subject: Re: [gmx-users] ed
raham wrote:
> > - Original Message -
> > From: Nuno Azoia
> > Date: Monday, March 9, 2009 21:52
> > Subject: Re: [gmx-users] editconf and genbox using method
> > To: Discussion list for GROMACS users
> >
> >> Hello!
> >>
> >> Your box
Mark Abraham wrote:
- Original Message -
From: Nuno Azoia
Date: Monday, March 9, 2009 21:52
Subject: Re: [gmx-users] editconf and genbox using method
To: Discussion list for GROMACS users
Hello!
Your box isn't rectangular. Your problem is just VMD display the gro
file w
- Original Message -
From: Nuno Azoia
Date: Monday, March 9, 2009 21:52
Subject: Re: [gmx-users] editconf and genbox using method
To: Discussion list for GROMACS users
> Hello!
>
> Your box isn't rectangular. Your problem is just VMD display the gro
> file with a rect
Hello!
Your box isn't rectangular. Your problem is just VMD display the gro
file with a rectangular shape. If you need to see your system properly
try to transform your .gro file in a .pdb file first, using trjconv.
Try trjconv -h to see the options
Nuno Azoia
On Mon, 2009-03-09 at 12:23 +0200,
- Original Message -
From: Marian Butu
Date: Monday, March 9, 2009 21:24
Subject: [gmx-users] editconf and genbox using method
To: gmx-users@gromacs.org
> editconf -f pep1 -o -bt octahedron -d 0.3 -c
This command line should provoke some warnings at least. Have a look at them,
and a r
Chih-Ying Lin wrote:
Hi
The flag of editconf -density has the default value 1000
editconf -densityreal1000Density (g/l) of the output box
achieved by scaling
But, my system is running on D2O not H2O
Earlier I did not notice this flag and simply use the command editconf
to crea
x in the
> output pdb.
>
> Berk
>
>
>> Date: Fri, 7 Nov 2008 12:13:55 +0100
>> From: [EMAIL PROTECTED]
>> To: gmx-users@gromacs.org
>> Subject: Re: [gmx-users] editconf/genbox problem in Gromacs 4.0
>>
>> Many thanks to Bert and Xavier.
>>
>>
gmx-users@gromacs.org
> Subject: Re: [gmx-users] editconf/genbox problem in Gromacs 4.0
>
> Many thanks to Bert and Xavier.
>
> >> Dear gmx-users,
> >>
> >> I have encountered a similar editconf/genbox problem posted by Matt
> >> Danielson on 14
Many thanks to Bert and Xavier.
>> Dear gmx-users,
>>
>> I have encountered a similar editconf/genbox problem posted by Matt
>> Danielson on 14 October:
>> I 'm using Gromacs 4.0 (installed on MacOS).
>>
>> 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o
>> may_protein_box.pdb
>
> use
On Fri, 7 Nov 2008 11:23:14 +0100
"Caterina Arcangeli" <[EMAIL PROTECTED]> wrote:
Dear gmx-users,
I have encountered a similar editconf/genbox problem posted by Matt
Danielson on 14 October:
I 'm using Gromacs 4.0 (installed on MacOS).
1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -
Hi,
This is a known bug in 4.0.
It has been fixed for 4.0.1, which will hopefully be released today.
Berk
> Date: Fri, 7 Nov 2008 11:23:14 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] editconf/genbox problem in Gromacs 4.0
>
> Dear gmx-users,
>
> I have
[EMAIL PROTECTED] wrote:
Users,
I have recently upgraded from Gromacs3.3 to Gromacs4.0 and I seem to be
encountering a problem when trying to solvate a protein in a water box.
Editconf command:
editconf -bt octahedron -f prot2.pdb -o prot2_test.pdb -c -d 1.0
It works for me. Is your input fil
Hi Maria,
The answer is in the source code of course. But here's a python/pymol
function which does the same thing, and which I wrote after the
routine in editconf. It takes as input the definition as a list with
lengths x,y,z and angles a,b,c and returns the upper triangular
matrix:
def triclini
VENKATESH HARIHARAN wrote:
Hello all,
I am pulling a 17 amino acid peptide under constraint pulling. Some details:
v = 0.01 nm/ps
dt = 0.002 ps
steps = 25
total time = 500 ps
My question is: When generating the water box for the simulation, I
understand that the edge of the box should
marcos wrote:
Hi,
editconf -mead writes a .pqr with a format "%10.5f%10.5f%10.5f" while it
should be "%8.3f%8.3f%8.3f".
Also the charges and radius are written in "%8.4f%8.4f" while the
program pdb2pqr writes as "%8.4f%7.4f"
I changed line 167 of pdbio.c from:
strcpy(pdbform,"%-6s%5u %-4.4s %3.
3.3.1 and 3.3.2
IIRC in 3.1.4 it was ok
Marcos
On Wed, 2007-10-31 at 18:34 +0100, Ran Friedman wrote:
> Dear Marco,
>
> Which version?
>
> Ran.
>
> marcos wrote:
> > Hi,
> >
> > editconf -mead writes a .pqr with a format "%10.5f%10.5f%10.5f" while it
> > should be "%8.3f%8.3f%8.3f".
> > Also
Dear Marco,
Which version?
Ran.
marcos wrote:
> Hi,
>
> editconf -mead writes a .pqr with a format "%10.5f%10.5f%10.5f" while it
> should be "%8.3f%8.3f%8.3f".
> Also the charges and radius are written in "%8.4f%8.4f" while the
> program pdb2pqr writes as "%8.4f%7.4f"
>
> I changed line 167 of p
Hi Arneh,
>From the help of editconf (editconf -h) you could have seen that it
has no such option. It wouldn't be very hard to add it though...
Cheers,
Tsjerk
On 8/8/07, Arneh Babakhani <[EMAIL PROTECTED]> wrote:
> Hi,
>
> In editconf, there's an option -center which allows you to place the
> g
Shayla Fitzsimmons wrote:
I have a box which contains a slab of carbon (solid) that is centered within the
box. However, I want the slab to be at the very right side of the box - I know
I must use editconf -translate to do this, however I cannot seem to make it
work.
The slab is centered has th
mahbubeh zarrabi wrote:
Dear all
I have a pdb of my protein. I want to position of
protein in x,y and z relative to the bilayer .how can
i do by editconf?
rhanks
editconf -h (always a good start)
editconf -translate -n
__
editconf -h
editconf -translate ...
cat xxx.pdb >> yyy.pdb
and remove the TER and ENDMDL lines
Good luck,
Jochen
mahbubeh zarrabi wrote:
Dear gmx_users
I am trying to insert one alpha-helical peptide . I
created two pdbs, bilayer.pdb and peptide.pdb . how
can i were adjusted the peptide c
Why not copy the coordinates of the channel in to th lipid's file?
Itamr.
mahbubeh zarrabi wrote:
Dear gmx_users
I am trying to insert one channel peptide in lipid
bilayer. I created two pdbs, bilayer.pdb and
peptide.pdb . how can i were adjusted the peptide
coordinates using editconf to be
==Original message text===On Wed, 19 Jul 2006 10:18:30 EDT Isabella Daidone wrote:-d is not for centering. -d is the distance of the protein from the walls of the box. Hi,when using editconf -d with gromacs version 3.3, it seems that the protein is not at the center but at
Beniamino Sciacca wrote:
Hi!
I've another question:
I've a DNA molecule, and I make a rigid traslation of the entire system.
If I try to display the new molecule with VMD, it doesn't display anything!
Instead if I run editconf on the new traslated molecule VMD works and I
see the molecule, but u
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