Try "genbox -cp *.gro -ci dmso.gro -p *.top -o *.gro"
Gro file for dmso comes built-in with gromacs 3.3. As Justin has directed,
forcefields do matter.
On 19/08/2008, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>
>
>
> prasun kumar wrote:
>
>> dear users
>> I am trying to run the simulation fo a
I am using the forcefield 43a2
option number 2 ie improved alkane dihedrals and i am using the same
dmso.gro and dmso.itp file that is given in the share/top file of
gromacs.but it is also right that the atom names are not matching in rtp
file.
I tried by replasing SDmso by SD in rtp file its not
Hi Parthiban,
Well, it was the best possible shot in the dark. Then please enlighten
us with more information: What is your command line? What platform do
you use? Which compiler? When did it work? What system?
Cheers,
Tsjerk
On Tue, Aug 19, 2008 at 5:55 AM, M.Parthiban <[EMAIL PROTECTED]> wrot
> prasun kumar wrote:
>> dear users
>> I am trying to run the simulation fo a protein/DMSO system,Its working
>> well till genbox but while running GROMPP I am gettin a fatal
>> error,which is
>> atom type 'SD' not found.
>> SD is given in the gro & itp file of DMSO.
>> what should I do to overcome
Please also note that *do_dssp* is part of the gromacs suite, and is
basically a wrapper around the third-party program *dssp* from CMBI,
calling it for every frame and processing the output. do_dssp relies
on the environment variable DSSP for locating dssp.
Tsjerk
On Mon, Aug 18, 2008 at 9:07 PM
Hi everybody,
I had run a long 100ns simulation on a tripeptide using
opls/aa force field and
spc water model.
I got a few microstates.
Then I tried to run simulation on the same system using charmm force field and
tip3p water
model.
However I couldn't find the microstate
hi
trjconv_mpi -f dimer_md.trr -o dimer_md.xtc (command which i used)
Linux (Platform)
Cluster machine (30 nodes, 1 node = 4 processor)
again i want you to know that my molecule is dimer with a small ligand
which gives error.
my molecule alone dosent gives error
thanks
Parthiban
> Hi Parthiban
hi
trjconv_mpi -f dimer_md.trr -o dimer_md.xtc (command which i used)
Linux (Platform)
Cluster machine (30 nodes, 1 node = 4 processor)
again i want you to know that my molecule is dimer with a small ligand
which gives error.
my molecule alone dosent gives error
thanks
Parthiban
> Hi Parthiban
I have already included the dmso.itp file.still I am getting the error
atom type SD not found
thanx in advance for helping me
--
PRASUN (ASHOKA)
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Please
prasun kumar wrote:
I have already included the dmso.itp file.still I am getting the error
atom type SD not found
thanx in advance for helping me
I don't know why (grompp?) is looking for atom type SD, when the atom *type* is
SDmso, but the atom *name* is SD. Are you sure you have made no
Hi all,
Is anybody has already done umbrella sampling for a free energy calculation?
There are some theoretical documentation but not so much information on
how to do that in practice. For me it's the first time. could anybody know
how for pulling or approaching two biomolecules and step simulation
Ah, sure, now we know!
Well, actually I almost confirmed my suspicion, just searching for
libc.so.6 in the archives. But first, you might want to read
http://www.catb.org/~esr/faqs/smart-questions.html
Then, you can continue with
http://www.gromacs.org/pipermail/gmx-users/2007-November/030605.html
[EMAIL PROTECTED] wrote:
Hi all,
Is anybody has already done umbrella sampling for a free energy calculation?
There are some theoretical documentation but not so much information on
how to do that in practice. For me it's the first time. could anybody know
how for pulling or approaching two bio
Thanks Justin for your reply.
In fact I did look that references and discussion you mentioned and actually
my e-mail was induced by them because I wanted to put some conclusions in a
straight bottom line. I've been even reading Amber manual about their
implementation for pressure and temperature c
> I have already included the dmso.itp file.still I am getting the error
> atom type SD not found
> thanx in advance for helping me
So everything should work. Either you didn't include corresponding
topology or you included something else to conflict.
Start your pursue from the very beginning. Ty
Dear Berk,
Thanks for your attention.
I don't know how familiar are you to amb2gmx and ffamber port to GMX. I am
just learning since I am trying to test an application that is related to
amb2gmx and ffamber (acpypi).
So, for Amber MD (MD to contrast with FF), Generalised Amber Force Field
(GAFF)
Alan wrote:
Thanks Justin for your reply.
In fact I did look that references and discussion you mentioned and
actually my e-mail was induced by them because I wanted to put some
conclusions in a straight bottom line. I've been even reading Amber
manual about their implementation for pressur
Hi,
You are on the right track .actually the problem lies with dmso.itp
which comes with original gromacs package...in that one column of mass is
missing just after column of charge value...so you just add them and then it
will work fine. (For hint you go through meoh.itp!)
with regards
anil
Hi,
I don't know if any thinking went into the (non) case specifity of atom types.
Nearly all string comparisons in Gromacs are not case specific.
For things like atom names this makes sense.
We could change the atom type comparisons to case specific.
I think that all force field files supplied w
thank you, check the site given in the post but there's no tutorial but i
least the dissertation of the guy doing those calculations, i could check
that.
thanks for suggesting me
geraldine
On Tue, August 19, 2008 1:15 pm, Justin A. Lemkul wrote:
>
>
> [EMAIL PROTECTED] wrote:
>> Hi all,
>> Is a
If a user could be assured that they would obtained the same microstates, even in an infinite simulation, then we could
finally get rid of the multitude of ff's and pick 'one' since they would all agree. However, this is not the case. Therefore
your assumption that you *should* get the same answe
From: [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Subject: RE: [gmx-users] charmm and oplsaa simulation results don't match
Date: Tue, 19 Aug 2008 10:47:02 +0200
Hi,
There are two main issues here.
One is sampling. I don't know what the correlations times in your systems are.
You say you o
hi,
Thanks for the suggestions. Actually the microstates are revisited in the
100ns span and one of them is occupied for longer time span than the others.
I had broken the 100ns trajectory(oplsaa) in 3 parts and took starting
structures from each of them and run simulations and obtained comp
Dear all,
I have just started learning gromacs to implement on a bead-spring
polymer system mainly to study hydrophobic collapse. While I am going
through the manual in detail, I have the following questions/confusions.
1. Which force field would be best to study such a system? Currently I
am us
Hello, I've searched the archives in search of an answer for my problem and
was able to solve only part of the problem.
I am working with a DNA/Protein system with AMBER99 forcefield.
The first problem is
"...Generated 2628 of the 2628 non-bonded parameter combinations
Generating 1-4 interactions:
water is part of the ff, therefore see previous comments of Berk and myself. For a reference, see Ponder and Case 2003
(http://www.ncbi.nlm.nih.gov/pubmed/14631816), and while one of the pmfs that they present is quantitatively incorrect, the
conclusions are valid: the different protein/water ff'
Ragnarok sdf wrote:
And the second error is the total system carge which is a non integral
charge.
I've looked for the " ERROR 0 [file "1VKX_C.itp", line 420]:
No default Bond types" solution but no one seams to have had the same
problem as I.
Not entirely true, they just haven't had th
I have added a mixture of oxgen and nitrogen to a simulation with a cnt.
The oxygen and nitrogen use morse potentials and the cnt uses the encad
force field. Previously I simulated the cnt with the default water and it
worked well. When using my "air" mixture the cnt collapses even if a small
numb
Hi, everyone:
I met a problem when I try to use the trjcat -demux to connect
trajectory files of REMD. I use 68 replicas for REMD simulation, and use
demux.pl script to get the replica_index.vgx file. Then I try to use the
trjcat -f traj*.xtc -demux replica_index.xvg to get a continuous
trajctory
Dear justin
I made topology top for tfe with gromos53a5.and I solvated in spc and
40molecule tfe.I includeed tfe.itp in topology.but when I do grompp I
get this error.(I edit the name of atoms with name in rtp file HT)
Generated 165 of the 1596 non-bonded parameter combinations
ERROR 0 [file "topo
Di Pan wrote:
Hi, everyone:
I met a problem when I try to use the trjcat -demux to connect
trajectory files of REMD. I use 68 replicas for REMD simulation, and use
demux.pl script to get the replica_index.vgx file. Then I try to use the
trjcat -f traj*.xtc -demux replica_index.xvg to get a co
Andy Shelley wrote:
I have added a mixture of oxgen and nitrogen to a simulation with a
cnt. The oxygen and nitrogen use morse potentials and the cnt uses the
encad force field. Previously I simulated the cnt with the default water
and it worked well. When using my "air" mixture the cnt colla
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