Hi,
I was trying to use g_rdf analysis tool to
calculate the structure factor of
a polymer I am simulating. I have generated own
..itp files for the polymer and the simulation is going
ok. But, whenever, I am trying to use g_rdf tool to
calculate the structure factor, it returns the
followi
Dear sir :
In fact, I have a complex structure(which contains protein and chromophore),
though I have known the usual procedure dealing with ligand or drug in the
gromacs, such as Prodrg server. Now I want to use Amber force field, and must
deal with chromophore molecule in the complex using a
OZGE ENGIN wrote:
Hi all,
I am trying to understand what type of distance can be used with g_cluster?
In the manual, it is written that RMS deviation after fitting or RMS deviation of atom-pair distances can be used to define the distance between structures in the first paragraph.
However, i
xi zhao wrote:
> Dear sir :
> In fact, I have a complex structure(which contains protein and
> chromophore), though I have known the usual procedure dealing with
> ligand or drug in the gromacs, such as Prodrg server. Now I want to use
> Amber force field, and must deal with chromophore molecule
Easily, I have a pdb complex(pdb: 1O5P), I want to produce corresponding gro
top files, but I can only produce chromophore gro and top file using amb2gmx.pl
.Are you clear ?
Mark Abraham <[EMAIL PROTECTED]> 写道： xi zhao wrote:
> Dear sir :
> In fact, I have a complex structure(which contains p
xi zhao wrote:
> Easily, I have a pdb complex(pdb: 1O5P), I want to produce corresponding
> gro top files, but I can only produce chromophore gro and top file using
> amb2gmx.pl .Are you clear ?
No. If you have a structure file already, then you need to read what I
wrote earlier. If you don't
Dear sir:
Is my english weak? I want to simulate pdb:1O5P (www.rcsb.org), I use amber
force field parms in the gromacs. Under this condition, pdb2gmx can not produce
chromophore top in the pdb,so I use antechamber and amb2gmx.pl to produce
chromophore gro and top files accoding to ffamber webs
Dear sir :
In fact, PRODRG can not produce chromophore top files properly, so I have to
give up gromos force field! The normal force field does not have params about
chromophore.
"Justin A. Lemkul" <[EMAIL PROTECTED]> 写道：
Search for John Kerrigan's enzyme-ligand tutorial. It explains in cl
Search for John Kerrigan's enzyme-ligand tutorial. It explains in clear detail
everything you will need to do. Ignore the part about using PRODRG for your
chromophore, as you apparently already have this information from antechamber.
For the future, it would be more clear to post this type of i
xi zhao wrote:
> Dear sir :
> In fact, PRODRG can not produce chromophore top files properly, so I
> have to give up gromos force field! The normal force field does not have
> params about chromophore.
See http://wiki.gromacs.org/index.php/Exotic_Species
Mark
___
Thank you Mark for your feedbacks.
There is one more point that is not clear to me for the output of g_cluster, In
the second column of the "cluster.log" of g_cluster, the same rmsd values are
indicated for different clusters. What does it mean? Although these clusters
have the same cut-off val
Hi all,
I guess this is directed towards the developers. Thanks to David Mobley, I was
able to determine that my free energy calculations were victim of a PME bug in
version 3.3.1. In the Bugzilla, Berk commented that the issue had been
resolved for the upcoming release of versions 3.3.3 and 4.0
Dear GMX users,
I want to prepare .gro and topology files starting from the .pdb file
for a polyethylene chain , whose residue is not defined in .rtp, .hdb.
and .tdb files. I have defined a new residue in ffoplsaa.rtp file as
follows
[ Eth ]
[ atoms ]
C1opls_136-0.1201
H
Hi Justin,
I can understand that you want your "forward" and "reverse" direction
results to be equal for verification reasons. But keep in mind that
there really is no "forward" or "reverse" direction when doing TI on
separately equilibrated (i.e. independent for every lambda) starting
stuctures (
Hi Ozge,
Not yet, since we came up with the idea during biophysical society,
but with a bit of luck it should be already this fall!
Cheers,
Erik
On Feb 16, 2008, at 9:40 AM, OZGE ENGIN wrote:
Hi Erik,
Did you put up a registration page for the workshop?
Could you give information, if the
Thanks for the input and useful information, Jeroen. I am trying to
parameterize some new molecules for use in my future work, so I would like to
take as much care as possible in getting things right!
-Justin
Quoting van Bemmelen <[EMAIL PROTECTED]>:
> Hi Justin,
>
> I can understand that you
Hi,
I have added missing atoms to my pdb file through servers of WHATIF,when I use
the force field option then the following output comes in shell console:
Fatal error:
Residue 'GTP' not found in residue topology database
and the following files are created:
2a5f.top 2a5f_A.itp 2a5f_B.itp posr
s lal badshah wrote:
Hi,
I have added missing atoms to my pdb file through servers of WHATIF,when
I use the force field option then the following output comes in shell
console:
Fatal error:
Residue 'GTP' not found in residue topology database
and the following files are created:
2a5f.top 2a5
Hi,
Oops - I happened to only post this to the gmx-developers list first:
I have put up a somewhat primitive information & registration page
about the Stanford workshop at
http://www.gromacs.org/stanford2008/
As I mentioned on friday, the space is somewhat limited (30-35
participants),
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