Hello there,
I am trying to run pdb2gmx on 3bzu.pdb file and got the following error
Opening library file /usr/share/gromacs/top/ffG43b1.rtp
Opening library file /usr/share/gromacs/top/aminoacids.dat
Reading 3bzu.pdb...
WARNING: all CONECT records are ignored
Read 'CORTICOSTEROID 11-BETA-DEHYDROGE
Hey Chris
When I downgraded to gcc 3.X I specified which compiler to use with CC=
and CXX= then my log was 4.X-free.
Have you tried that?
I had not considered that. Thanks for the advice David,
Chris.
David
Message: 3
Date: Mon, 11 Aug 2008 16:48:32 -0400
From: Chris Neale http://www.gro
Hey Chris
When I downgraded to gcc 3.X I specified which compiler to use with CC=
and CXX= then my log was 4.X-free.
Have you tried that?
David
Message: 3
Date: Mon, 11 Aug 2008 16:48:32 -0400
From: Chris Neale <[EMAIL PROTECTED]>
Subject: [gmx-users] ensuring that compilation used gcc 3.x
T
Hello,
I am attempting to compile gromacs using gcc 3.x and I would like to
confirm that I have actually obtained what I intended. In order to do
this, I have set my path with the desired version of gcc first:
export PATH=/tools/gcc/3.4.6/bin:$PATH
However, I am not convinced that I am actua
You are right, I am using 3.3, sorry for this mistake. I will try the command
which you have mentioned with -center zero for a small number of frames i.e. -b
2000 -e 3000 and get back to you.
thnx,
Pri...
- Original Message
From: Justin A. Lemkul <[EMAIL PROTECTED]>
To: Discussion l
priyanka srivastava wrote:
Dear Justin,
Thanks a lot for replying back.
These are the two things that I have tried but still the peptide does
not come at the center:
1. trjconv -f complete_production.xtc -s test.tpr -o test.pdb -center
zero -b 22000
The "-center zero" flag is not an opt
Dear Justin,
Thanks a lot for replying back.
These are the two things that I have tried but still the peptide does not come
at the center:
1. trjconv -f complete_production.xtc -s test.tpr -o test.pdb -center zero -b
22000
Select group for centering
Protein
Select group for output
System
2.
priyanka srivastava wrote:
Dear All,
I really apologize for asking a peptide translation related question
again. I have a lipid-peptide system and I have already carried out the
production run for 20ns. The peptide has moved towards one of the edges
(I didnt specify comm-grps in the mdp fil
Christian Fufezan wrote:
Dear gmx users,
I am new to MD and working my way through some tutorials. I saw that
pdb2gmx has the "-inter" flag which is used to specify which
conformers/protonation stats should be used.
Is there a way in which this can be automatised ?
For example, lets say I
Dear All,
I really apologize for asking a peptide translation related question again. I
have a lipid-peptide system and I have already carried out the production run
for 20ns. The peptide has moved towards one of the edges (I didnt specify
comm-grps in the mdp file). I have to translate the pep
Dear gmx users,
I am new to MD and working my way through some tutorials. I saw that
pdb2gmx has the "-inter" flag which is used to specify which
conformers/protonation stats should be used.
Is there a way in which this can be automatised ?
For example, lets say I have a list.txt
HIS
Dear all,
I simulate pulling experiment with the AFM-option in GROMACS. I
calculate the forces from the .pdo file:
F = k_c (/spr/ - /pullg/)
with F the force, k_c the springconstant. spring is the position of the
spring and /pullg/ the position of the pullgroup. after the
bond-breakage the forces h
Dear all,
I simulate pulling experiment with the AFM-option in GROMACS. I
calculate the forces from the .pdo file:
F = k_c (/spr/ - /pullg/)
with F the force, k_c the springconstant. spring is the position of the
spring and /pullg/ the position of the pullgroup. after the
bond-breakage the forces h
Hi all!
I am quite new to Gromacs and am wondering why I can´t see any box
fluctuations during a NPT run of protein + urea solvent in dodecahedron. In
the energy output file I can see that the Box-X,Y,Z values only fluctuate
<1%.
However the pressure average is reasonably close to the ref_p valu
Biswaranjan Meher wrote:
Dear All,
I have a simple querry regarding the secondary structure analysis.
Using my_dssp I have done the secondary structure analysis for my
protein (all residues) of interest.
But I want to show the secondary structural changes for a / few
particular residues in t
Dear All,
I have a simple querry regarding the secondary structure analysis.
Using my_dssp I have done the secondary structure analysis for my protein
(all residues) of interest.
But I want to show the secondary structural changes for a / few particular
residues in the protein.
Is it possible to c
>large peak at around 0.1 nm
It's intramolecular one. See help for g_rdf.
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
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On Sun, 10 Aug 2008, niharendu choudhury wrote:
Dear all,
I tried to calculate oxygen-hydrogen (O-H) rdf of SPC water from the
trajectory file, which I generated according to the instructions given in
the (web) tutorial on water. For O-H rdf i have generated the index file
for oxygens and hydro
Dear all,
I tried to calculate oxygen-hydrogen (O-H) rdf of SPC water from the trajectory
file, which I generated according to the instructions given in the (web)
tutorial on water. For O-H rdf i have generated the index file for oxygens and
hydrogens. Then I calculated rdf with
g_rdf -n
comm
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