OK thank you four kind response. And also thank you and the CHARMM team for
this geat job.
Stephane
---
On 10/9/13 11:28 AM, ABEL Stephane 175950 wrote:
> Hello Justin,
>
> Two quick questions, here
>
> - Since the lipid charmm36 parameters for lipids are already a
Hello Justin,
Two quick questions, here
- Since the lipid charmm36 parameters for lipids are already available in the
gromacs format on the GROMACS website (charmm36.ff_4.5.4_ref.tgz) from thomas
Piggot. Does it means that these files are considered as deprecated and all the
users are invit
Finally, I have resolved my (little) problem: I used CHARMM-GUI to constructed
the membrane, removed the TIP3 water molecules and then resolvate the bilayer
with TIP4P/2005 water molecules. The simulation seems to work.
Stephane
On 9/23/13 10:23 AM, ABEL Stephane 175950 wrote:
> He
e Explicit Water Model Be Varied? J. Chem. Theory Comput. 2007, 3, 1550–1560.
Stephane
On 9/23/13 5:02 AM, ABEL Stephane 175950 wrote:
> Hello,
>
> Because I want to compare the simulation results (essentially water dynamic)
> with previous simulations of reverse micelles, micelle
t 10:36 AM, ABEL Stephane 175950
wrote:
> Hello all,
>
> It is not a gromacs problem "per se", but I hope that some gromacs users can
> help me. I would to do simulations of phospholipid bilayers with the
> TIP4P/2005 water model. I have downloaded in the Klauda&#x
Hello all,
It is not a gromacs problem "per se", but I hope that some gromacs users can
help me. I would to do simulations of phospholipid bilayers with the TIP4P/2005
water model. I have downloaded in the Klauda's website several bilayer starting
conformations. However, since CHARMM uses the
ues.
Stephane
--
Message: 4
Date: Tue, 3 Sep 2013 12:57:25 +0000
From: ABEL Stephane 175950
Subject: [gmx-users] Select atoms in a residue
To: "gmx-users@gromacs.org"
Message-ID:
<3e39b768bb199548ab18f7289e7534af1a880...@exdag0-b0.intra.cea.fr>
Content-Type: text/plain; ch
Hello all,
A Quick question below:
My peptide contains one trp, and i want to select only the atoms that form the
the indol ring. I would like a portable script for others systems that contain
also a peptide with one Trp residue. So I am not interesting to select the
corresponding atoms by t
Hello,
I have a done a lot of simulations of reverse micelles. For me to construct the
best model of preformed RM you can indeed use Packmol. But after that, you will
carry out out different equilibration stages to obtain stable reverse micelles.
>> I want to arrange charge, LJ parameter, hydro
Hi,
You indeed could use the g_rdf command like this (in the script)
g_rdf_mpi -f "$pathXTC" -s "$pathTPR" -n bOG_Micelle_RDF.ndx -norm -com -b
$timeBegin1 -e $timeEnd1 -o "$name1"_"$name2"_"$name3"_"$i"_original.xvg <
RadDensFunc_"$i".txt
Where in the RadDensFunc.txt file, i choose as the f
--
Message: 1
Date: Fri, 26 Apr 2013 07:58:12 +0200
From: XAvier Periole
Subject: Re: [gmx-users] Re: Martini with PME, temp two low (ABEL
Stephane 175950)
To: Discussion list for GROMACS users
Message-ID: <6d1fd74e-91bb-4c0c-95ce-e863924dd...@rug.nl>
Conten
: 1
Date: Fri, 26 Apr 2013 07:58:12 +0200
From: XAvier Periole
Subject: Re: [gmx-users] Re: Martini with PME, temp two low (ABEL
Stephane 175950)
To: Discussion list for GROMACS users
Message-ID: <6d1fd74e-91bb-4c0c-95ce-e863924dd...@rug.nl>
Content-Type: text/plain; charset=us
:00 +
From: ABEL Stephane 175950
Subject: [gmx-users] Re: Martini with PME, temp two low
To: "gmx-users@gromacs.org"
Message-ID:
<3e39b768bb199548ab18f7289e7534af1a818...@exdag0-b0.intra.cea.fr>
Content-Type: text/plain; charset="us-ascii"
@ Vitaly
of course.
energy.
On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950 wrote:
> Hello Xavier,
>
> Thank you for your response.
>
>>> nstlist = 10 and the rlist = 1.0
> My mistake, i did not changes these values when i switched to PME,
>
> I have rerun the simulations for 400 ps i
; As a side note (not relevant for PME) the mix of nstlist = 10 and the
> rlist = 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and
> rlist=1.4 if nstlist =10.
>
> On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950
> wrote:
>
> > Hello all,
> >
>
0.0e+00 -2.04448e+04
W-W0.0e+00 -3.88078e+02
Stephane
--
Message: 4
Date: Thu, 25 Apr 2013 13:26:32 +
From: ABEL Stephane 175950
Subject: [gmx-users] RE : gmx-users Digest, Vol 108, Issue 154
To: "gmx-users@gromacs.org"
at 1:10 PM, ABEL Stephane 175950 wrote:
> Hello all,
>
> I am trying to test the martini force field with PME for a charged system
> that contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa.
> My system works well, if i use the standard shift parameters (correct
Hello all,
I am trying to test the martini force field with PME for a charged system that
contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. My
system works well, if i use the standard shift parameters (correct temp, and
pressure). But for for the simulation with PME , the
Thank you Tsjerk for your quick response.
A bientot
Stephane
--
Message: 2
Date: Tue, 26 Feb 2013 16:53:51 +0100
From: Tsjerk Wassenaar
Subject: Re: [gmx-users] How to differenciate Decane and Dodecane with
the Martini force field
To: Discussion list f
Hello all,
Sorry if it is not the right place to ask the question, but i have a doubt
about the topology for alkanes with MARTINI
Since in Martini
- the default mapping is 4 AA -> 1 bead
- that in the martini_"v2.0_solvents.itp file" it is stated that the DECANE has
the same topology as dode
ABEL Stephane 175950
wrote:
> Hello All,
>
> It is a newbie question here, but I can not find a clear response. I would
> like to create a simple box of pure DECANE for MD with the Martini force
> field. I have tried do that with genbox (as for AA force field)
>
> genbox_m
Hello All,
It is a newbie question here, but I can not find a clear response. I would like
to create a simple box of pure DECANE for MD with the Martini force field. I
have tried do that with genbox (as for AA force field)
genbox_mpi -cp 1_CG_DECANE.pdb -ci 1_CG_DECANE.pdb -o CG_DECANE_box.gro
gle it. If it
> is not in Gromacs format you can just write a couple 6 liner scripts to
> re-format it by parsing into the gromacs format,
>
> Stephan Watkins
>
> Original-Nachricht
> > Datum: Wed, 13 Feb 2013 21:25:33 +
> > Von: ABEL Stephane
Abel,
Theres a link I on the gromacs web site to ATB, or you can google it. If it is
not in Gromacs format you can just write a couple 6 liner scripts to re-format
it by parsing into the gromacs format,
Stephan Watkins
Original-Nachricht
> Datum: Wed, 13 Feb 2013 21:25:
Hello all,
Does somebody know where i can find the latest GROMOS force field (i.e.
GROMOS54A8) described in [1] in the GROMACS format (gromos54a7.ff) ?
[1] Reif et al. J. Chem. Theory Comput. 2013, 9, 1247−1264 doi:
http://pubs.acs.org/doi/citedby/10.1021/ct300156h
Thank you
Stephane--
g
Hello,
Is it correct for you that in your topolgy file, some atoms have wrong mass
(i.e. C7 and C9 have a mass of 15.035 instead of 14.027) in your DECAN
molecule ? Are they at the end ?
Stephane
--
Message: 3
Date: Thu, 7 Feb 2013 19:13:11 +0330
From: Ali Al
Dear All,
I would like to compute the end to end distribution for different parts (i.e.
hydrophobic and the polar) of several detergent molecules. I know that
g_polystat can do the job and indeed i can obtain the end-to-end distance of
the whole molecule (at least for the distance vs. time)
Hello,
This is a very nice and interesting work, Michael. Thank you for the efforts
you made in writing this paper. I hope you will publish it.
Best
Stephane
Hi, all-
There are some issues with MTTK + constraints that are being worked
out for 4.6.
f it was not clear in my previous message
Stephane
--
Message: 1
Date: Mon, 19 Nov 2012 16:14:48 +
From: ABEL Stephane 175950
Subject: [gmx-users] which version it is
To: "gmx-users@gromacs.org&quo
Hi,
Probably the "CHARMM27_protein+Charmm36_lipids" version. AFAIK, the second
version was not already converted in GROMACS format.
Stephane
---
hello:
I found a charmm36.tar.gz in Gromacs website
GROMACS 4.5.4 version of the CHARMM36 fo
Hi,
CHARMM22star FF is a "fork" of CHARMM27 ff for proteins with several changes in
some diedral parameters. It should be compatible with the others CHARMM
parameters for biomolecules.
Stephane --
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-user
Hello,
Can you explain why you want to use/convert the RB form for your alkane
dihedral angles instead of the usual CHARMM dihedral potential form available
in charmm force field library available in the GROMACS distribution ?
Stephane
--
gmx-users mailing listgmx-users@gromacs.org
http://
Hi
Since you want to use the AMBER force for your calculations, you will need to
compute the RESP charges for your new residue (unprotoned TYR) and add the
charges in your *rtp file. To compute the charges, you can use the RED.Server
(http://q4md-forcefieldtools.org/REDS/).
It is not easy, s
Daer all,
I am trying to compute the transition times (TT) for all the angles in
dodecane in the bulk (216) with gromacs 4.5.5
I have constructed an index file with all angles
(C1C2C3C4C9C10C11C12) and for all the nine angles (C*C*C*C*) and use
the following command for ea
Dear all,
I would like to compute the number of gauche <--> trans transitions (per
ns) for for several alkanes. I know that I can use g_angle with -ot flag. But
in the manual it is stated that this command works only for dihedrals with
multiplicity 3.
In CHARMM36 force field, for exampl
Hi,
Here, my 2 cents worth. You can also estimate (roughly !!) the HB energy
between two groups (say NH---CO) by using the Kabsch and Sander function
described in Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577−2637).
Quoting:" E = qlq2(1/r(0N) + l/r(CH) - l/r(OH) - l/r(CN))*f with q1 = 0
Hi Patrick,
Your response is indeed more useful that my previous answer and with
interesting links
thank for the pointers
Stephane
--
Message: 4
Date: Fri, 18 May 2012 10:51:35 +0200
From: Patrick Fuchs
Subject: Re: [gmx-users] What is the autocorrelation time
Hi Chris,
Probably these links give you simple and clear response for your question
http://idlastro.gsfc.nasa.gov/idl_html_help/Time-Series_Analysis.html
and
http://www.statsoft.com/textbook/time-series-analysis/
HTH
Stephane
--
gmx-users mailing listgmx-users@gromacs.org
http://lis
Hi,
In my opinion use Amber ff to simulate phospholipids is a bad idea. An
alternative is to use GAFF with the good RESP charges.
See these papers where several phospholipids are simulated with the GAFF ff.
(1) Siu, S. W. I.; Vácha, R.; Jungwirth, P.; Böckmann, R. A.; Shirley, S. W.
I.; Rob
rtypes ]
;;for protein
H1 H1 1 0.247135000 0.006568880 ;the epsilon is divided
by 10
;;for sugar
H1S H1S 1 0.24713500 0.010948133 ;the epsilon is divided
by 6
Thanks for your time,
Regards
Sai
On Mon, Sep 5, 2011 at 11:33 AM, ABEL Stephane 175950
wrote:
>
Hi Chris, Druz
Thank you very much for your reply. Indeed I have read several papers where the
diffusion of water at the membrane surface have been computed. Since the
diffusion of the interfacial water is an useful properties to examine the
micelle/surface irregularities, I would hope that th
Hi GMXusers,
I know that the g_energy can be used to compute/estimate the adiabatic and
isothermal compressibility values of the simulation box when the TEMP, volume
and nmol values are given. nmol can be easily given for a pure solvent but when
I have a two (or more) different species in the m
Dear All,
Below a little update and results about the application of half double pair
list method to scale properly the Coulombic 1-4 interactions in case of a
system where the AMBER99SB (fudgeLJ=0.5 and fudgeLJ=0.8333) and GLYCAM06
(fudgeLJ=1.0 and fudgeLJ=1.0) force fields are combined.
I ha
Chris,
Thank you for your confirmation. I did the changes. I am currently doing some
tests, I will send you a feedback about the results off-list (if you want)
shortly.
A bientôt
Stéphane
Message: 1
Date: Thu, 01 Sep 2011 14:38:53 -0400
From: chris.
Thank you Nishap for the references and Justin for pointing out the issues with
the dihedral angles.
Bye
Stéphane
ABEL Stephane 175950 wrote:
> Dear All,
>
> I am looking for a topology file (*.itp) for trehalose for simulations with
> the GROMOS53A6 (or more recent). Does s
Dear All,
I am looking for a topology file (*.itp) for trehalose for simulations with the
GROMOS53A6 (or more recent). Does someboby know where I can find it?
Thank you in advance for your help
Stéphane
--
Stéphane Abel, PhD
CEA Saclay
DSV/IBITEC-S/SB2SM & CNRS
Dear All,
I would like to perform some MD of disaccharides in water using GROMACS and the
new ff for sugars GROMOS45ACARBO from Hansen and unenberger(JCC, 32, 6, 2011).
Does somebody have these parameters in the GROMACS format (e.g. the *.itp
files) and want to share them with me.
Thank you
HI shahid,
you can also use the following formula
((N_chaps/(Nw*Vw))/6.02214179)*1=density you want in (Mol)
Where
- N_chaps is the number of chaps mol. 614.88 g (from wikipedia)
- Nw : number of water mol.
- Vw : volume of water (30 A3 in ambiant condition) ~
- 6.02214179 Avogadro numb
Hi Justin
As i have said in the message the pdb file needs probably some (small) changes.
emacs (or vi) and vmd or rasmol are our friends ;)
Below the pdb file in the correct format (tested with rasmol and vmd)
REMARK Accelrys Discovery Studio PDB file
REMARK Created: Mon Jan 10 20:
Hi Marcelo,
I can send you a pdb file of this molecule construct with Discovery visualizer
2.5 if you are interested. You will need only to change the atom names and a do
several minimzation steps.
Stephane
On Mon, 2011-01-10 at 17:59 +, Marcelo Silva wrote:
> Hi everybody,
>
> I wa
Re hi Marcelo,
Below the perfluorohexane molecule in the pdb format construct with the
Discovery Studio Visualizer v2.5
REMARK Accelrys Discovery Studio PDB file
REMARK Created: Mon Jan 10 20:52:13 Paris, Madrid 2011
HETATM1 C1 0 -11.336 -0.581 0.212 1.00 0.00
Hi Hengameh
Below, my TFE.gro (with the atom names for CHARMM Cgenff) i used it previously
for md. You can easely translated in others ff you use
9
1TFE O11 0.397 1.386 1.484 0.4892 -0.3653 -0.3242
1TFEHO12 0.446 1.346 1.557 0.8382 -0.5070 -0.6322
1TFE
dOd9+IZ7KrmZ1u
2VgAoIPTQGVxyrmDUXi5PbPPg5tCr7h2
=PBOI
-END PGP SIGNATURE-
--
Message: 2
Date: Thu, 14 Oct 2010 17:54:02 +0200
From: "ABEL Stephane 175950"
Subject: [gmx-users] Questions about REMD calculations
To:
Message-ID:
Content-Type: te
Dear all,
I come back to you for several questions about the futures replica-exchange
calculations that i would like to perform. The system of interest will contain
12 peptides (with 7 residues each) and 4 water molecules, it come from a
previous MD performed in NPT ensemble. With these s
en exchanges is in general
equal to that of the coldest replica, since that will be at the highest
density (unless you go below the density maximum of water :)).
>/
/>/ XAvier.
/>/
/>/ On Oct 13, 2010, at 11:36 AM, ABEL Stephane 175950 wrote:
/>/
/>>/ Dear All,
/>>
Dear All,
For a futur project, I would like to perform the REMD calculations with
GROMACS4.5.X. To have an estimation of CPU time required, I have a naive
question: What is the speed of REMD compared to a classic NPT MD ? I am aware
that the response depends a lot of factor (number of replica,
in Gromacs (Mark Abraham)
--
Message: 1
Date: Thu, 30 Sep 2010 21:48:05 +1000
From: Mark Abraham
Subject: Re: [gmx-users] Re: Error : There is no domain decomposition
for
To: Discussion list for GROMACS users
Message-ID:
Content-Type: text/plain; charset="us-ascii"
- Origina
rease the number of node or CPU ?
> Thank you again for your help
> Stephane
ABEL Stephane 175950 wrote:
> Dear All,
>
> I am trying to do a MD of a system containing TIP3P water, a peptide, some
> glycolipids molecule and ions in a cubic box. The forcefield used is CHARMM
>
Yeah Justin, I have already read the comments related to the link before to
post in the mailing list. But I don't know how to correct this ?
Increase/decrease the number of node or CPU ?
Thank you again for your help
Stephane
ABEL Stephane 175950 wrote:
> Dear All,
>
>
Dear All,
I am trying to do a MD of a system containing TIP3P water, a peptide, some
glycolipids molecule and ions in a cubic box. The forcefield used is CHARMM and
are taken from previous MD. The bonded and nonbonded parameters was converted
in GROMACS manually because some parameters are not
OK you thank Justin for your explanation. Accordingly, I have changed the C*
and O* atom names in the pdb and now it works.
A bientôt
Stefane
ABEL Stephane 175950 wrote:
> You are right Justin,
>
> The 1O1 atoms and (others 1O2, etc.) are changed to O11, O21, etc. (?). Why
>
You are right Justin,
The 1O1 atoms and (others 1O2, etc.) are changed to O11, O21, etc. (?). Why
this problem happens ? Should I change the name of these atoms in the rtp and
pdb files ? Is a trick is available to avoid this "bad" translation ?
Stefane
ABEL Stephane 175950 wro
Dear all,
I have a very "common" problem when I try to convert a pdb file to a gro file
with the following command.
I use charmm27ff and gmx4.5.1.
pdb2gmx_mpi -f 1-bDM.pdb -o 1-bDM.gro -p 1-bDM.top -chargegrp
I obtain the following "commun" error :
"Atom O11 in residue bDM 1 was not fou
o-8859-1"
eps(charmm)*4.184=epsilon(Gromacs)
0.15*4.184=0.6276
Rmin/2(Charmm)*2/(2^1/6)=sigma(Gromacs)
2.27*2/(2^(1/6))=0.404468(nm)
Cheers,
Jianhui
Date: Fri, 24 Sep 2010 15:55:44 +0200
From: "ABEL Stephane 175950"
Subject: [gmx-users] CHARMM -> gromacs epsilon and sigma con
Hi all,
I would like to add new atom types in the charmm27.ff for futures simulations
of glyolipids in water with gmx 4.5.1. I have finished to convert the bonded in
GROMACS format. However, I am little puzzled with the vdW paramaters. I would
like to know how to convert them (i.e. what are t
Thank you Mark for your response
If understand well, I should only to copy these additional the values in the
[atomtypes] section of the ffcharmmnb.itp file without others
modifications/corrections. It is correct ?
Stefane
> Hi GMX users,
>
> I would like to perform MD with new developped
Hi GMX users,
I would like to perform MD with new developped CHARMM parameters in GROMACS.
Since these parameters are new, they are not presents in the ffcharm*.itp files
given in the of charmm27.ff in the latest GMX distribution. So I have already
made the conversions for the bonded paramete
It works !!!
Thank you Justin
A bientôt
Stefane
ABEL Stephane 175950 wrote:
> Hi all,
>
> I have simulated a system containing 55 DPC molecules, a peptide some ions
> and water in a cubic box. Initially all molecules were placed randomly in the
> box. As expected during the
Hi all,
I have simulated a system containing 55 DPC molecules, a peptide some ions and
water in a cubic box. Initially all molecules were placed randomly in the box.
As expected during the simulation all the DPC molecules aggregate to form a
stable micelle with the peptide located at the micel
Ok thank you all for your suggestions
A bientot
>
> ABEL Stephane 175950 wrote:
>> Hi everybody,
>> I am doing some analysis of the interpeptidique hbonds (INTRHB)
>> during the aggregation in beta fuof 4 heptapeptides in water
>> I have defined in a index fi
Hi everybody,
I am doing some analysis of the interpeptidique hbonds (INTRHB) during the
aggregation in beta fuof 4 heptapeptides in water
I have defined in a index file the Acceptor-Donor-Hydrogen atoms list for the
28 INTRHB like this
NH--CO
[intra_hbds]
4 17 5
18 26 19
27 43 28
44 52 4
Tue, 02 Feb 2010 01:54:13 +1100
From: Mark Abraham
Subject: Re: [gmx-users] perl scripts to convert CHARMM ff in GROMACS
To: Discussion list for GROMACS users
Message-ID: <4b66eb15.5090...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 02/02/10 01:29, ABEL Stepha
Hi GMXusers
I am testing the parameters of CHARMM, it works fine for lipids and protein.
This is a great job, thanks to the devellopers But i would like to add some new
molecule for solvent (e.g. for TFE) The atom types of TFE are present in the
ffcharmm27bon.itp available in latest port (c32b1
Hi everybody
I am currently testing the CHARMM port for GROMACS pre4.1. I have downloaded
the c32b1_release_1.1.zip file http://www.dbb.su.se/User:Bjelkmar/Ffcharmm
(11:59, 23 Oct 2009). My protein protein have an acetylated N-terminus and
amidated C-terminus. According to the CHARMM force fiel
Thanks Justin
Indeed, It worked !!!
In french, one says: "je ne dormirai pas idiot ce soir".
Stéphane
>Thank you Roland for your response
>I have effectively downloaded from the
>http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz, the HEAD version
>of gmx Unfortunately, the unpacked dir
Dear GMX Users,
I ask this question in this mailing list since probably a user have already
encountered this similar problem. I would like to post-process my trajectory
with the command trjconv (in mpi mode). For this I use the following shell
command:
echo 0 | /usr/pbs/bin/mpiexec /scratch/
Hi gromacs users
I have a newbie question about the atom type in gromacs. I would like to
simulate a peptide with AMBER ff (ffamber03) in gromacs v.4.05 , so I have
downloaded the ffamber files and followed the explanation given in Sorin's lab
homepage. To neutralize my system i have added one
Thank you Mark for the advice,
I will take a look of this.
Stephane
Stephane Abel wrote:
> Hi gromacs users and experts
>
> I am doing some simulations using 8 CPU of solvate peptide (8 AA) in
> octahedron truncated box (5150) with SPC water with GMX 4.05. To
> simulate during a long time
OK thank you Omer, for you response
The group PROTEIN isn't very large as the group NONPROTEIN, therefore its
total kinetic energy fluctuates more.
--Omer.
On Wed, Sep 16, 2009 at 12:10, Stephane Abel wrote:
> tc-grps = Protein Non-Protein ; two coupling groups - more accurate
> tau_t = 0.4 0
Hi,
VMD uses a heuristic method to know if some atoms are connected. Sometimes the
method fails. To be sure (and see) the atoms are well connected in VMD, you
need to provided a psf file with your pdb/gro in VMD. So in your case you gro
files is correct (since you indicated that your system are
Thank you it works now
Stefane
> Hi gromacs users
>
> When I use the xpm2ps utility to made a ps graphic of the secondary structure
> with my xpm file, the graph obtained is show in portrait orientation and by
> consequence trucated because the page width is to small. How to change the
> orientati
Hi gromacs users
When I use the xpm2ps utility to made a ps graphic of the secondary structure
with my xpm file, the graph obtained is show in portrait orientation and by
consequence trucated because the page width is to small. How to change the
orientation of graph with xpm2ps (for example a
Hi Gromacs Users
My Problem with do_dssp is resolved : my do_dssp was strangely corrupted. After
recompilation it works well. Thank you for all people who helped me. See U soon
on this mailing list
Stefane
___
gmx-users mailing listgmx-users@grom
minutes is not to short to process one config indeed
the DSSP program take less than 2 seconds to compute the secondary structure of
the protein in 1HRC pdb file.
So i very frustrated...
Stefane
ABEL Stephane 175950 wrote:
> Hi Gromacs users
>
> After many try this weekend with m
ATOM 19 HB1 ASP 3 11.065 -4.008 -11.725 0.09 0.00
> ATOM 20 HB2 ASP 3 12.877 -3.652 -11.448 0.09 0.00
> ATOM 21 CG ASP 3 12.414 -5.579 -12.163 0.62 0.00
> ATOM 22 OD1 ASP 3 11.641 -5.923 -13.130 -0.76 0.00
> ATOM 23
0.00
> ATOM 22 OD1 ASP 3 11.641 -5.923 -13.130 -0.76 0.00
> ATOM 23 OD2 ASP 3 13.571 -5.997 -12.137 -0.76 0.00
>
> Thank you again for your kindly help
>
> Stefane
>
> ABEL Stephane 175950 wrote:
> > I used the following command
> >
-12.163 0.62 0.00
ATOM 22 OD1 ASP 3 11.641 -5.923 -13.130 -0.76 0.00
ATOM 23 OD2 ASP 3 13.571 -5.997 -12.137 -0.76 0.00
Thank you again for your kindly help
Stefane
ABEL Stephane 175950 wrote:
> I used the following command
>
> ./do_dssp -s test.SecStruc
.130 -0.76 0.00
ATOM 23 OD2 ASP 3 13.571 -5.997 -12.137 -0.76 0.00
Thank you again for your kindly help
Stefane
ABEL Stephane 175950 wrote:
> I used the following command
>
> ./do_dssp -s test.SecStruc.tpr with test.SecStruc.tpr is a pdb file with a
> part
Thanks David for his last response
I am a newbie in GROMACS command, and i have a question. What is the difference
between do_dssp and my_dssp ? found in some GROMACS tutorial. I can not find
the last one in the gromacs 3.3.2 distribution
Thank a lot
Stefane
___
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Quoting ABEL Stephane 175950 <[EMAIL PROTECTED]>:
> > Hi gromacs users
> >
> > For my work I have performed some simulations of a protein in wa
Hi gromacs users
In previous message Mark Abraham. said me that do_dssp tools can be used only
with a pdb file (thank to him ;))). I am newbie with gromacs (i came from the
ORAC MD world), so i have two questions
1 °) Can do_dssp can be used with "only" one pdb file with some configurations
> Hi gromacs users
>
> For my work I have performed some simulations of a protein in water with an
> other MD software not compatible with >GROMACS. And I would like to compute
> the time evolution of the secondary structure of my protein, I know that the
> >with >the xpm2ps tool give in gromacs
Hi gromacs users
For my work I have performed some simulations of a protein in water with an
other MD software not compatible with GROMACS. And I would like to compute the
time evolution of the secondary structure of my protein, I know that the
do_dssp tool in GROMACS is made for this. This too
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