should give you at starting point.
Jim
> -Original Message-
> From: gmx-users-boun...@gromacs.org
> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Nancy
> Sent: Friday, July 31, 2009 5:19 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Carbohyd
I used gzip to uncompress the file first:
# gzip -d topolbuild1_2_1.tgz
and then I used tar:
# tar -xvf topolbuild1_2_1.tar
This seems to work.
On Sat, Aug 1, 2009 at 6:05 PM, Justin A. Lemkul wrote:
>
>
> Nancy wrote:
>
>> Hello,
>>
>> I downloaded "topolbuild1_2_1.tgz" from the URL:
>>
Nancy wrote:
Hello,
I downloaded "topolbuild1_2_1.tgz" from the URL:
http://www.gromacs.org/@api/deki/files/40/=topolbuild1_2_1.tgz
However, when I tried to decompress the file, I received the following
error message:
# tar -xvf topolbuild1_2_1.tgz
You have to unzip it as well, i.e.:
Hello,
I downloaded "topolbuild1_2_1.tgz" from the URL:
http://www.gromacs.org/@api/deki/files/40/=topolbuild1_2_1.tgz
However, when I tried to decompress the file, I received the following error
message:
# tar -xvf topolbuild1_2_1.tgz
tar: This does not look like a tar archive
tar: Skipping to
On Fri, Jul 31, 2009 at 5:19:19 PM, Nancy wrote:
> If it necessary to manually create force field parameters for each
molecule, then how can one run a
> simulation involving a number of
arbitrary molecules (e.g. a set of mono and disaccharides) for
> which
there are no existing force fields?
>
>
Hi Nancy,
I think that the atom C1 in residue TRP 1 does not exist in rtp entry. In
other words, atom C1 is not understood by the software. You should change the
atom type in order to be understood. I have a question, how do you obtain the
URL about trehalose. Because I want to some polyols f
Nancy wrote:
High-throughput "in silico" screening (e.g. for ligand-protein binding)
has been performed on a number of systems. How are such automated
simulations performed (I assume they utilize molecular dynamics)?
I doubt that large classes of ligands have been done effectively with MD
High-throughput "in silico" screening (e.g. for ligand-protein binding) has
been performed on a number of systems. How are such automated simulations
performed (I assume they utilize molecular dynamics)?
On Fri, Jul 31, 2009 at 5:47 PM, Justin A. Lemkul wrote:
>
>
> Nancy wrote:
>
>> If it n
Nancy wrote:
If it necessary to manually create force field parameters for each
molecule, then how can one run a simulation involving a number of
arbitrary molecules (e.g. a set of mono and disaccharides) for which
there are no existing force fields?
Do you know of any other MD software pac
If it necessary to manually create force field parameters for each molecule,
then how can one run a simulation involving a number of arbitrary molecules
(e.g. a set of mono and disaccharides) for which there are no existing force
fields?
Do you know of any other MD software package that is capable
Nancy wrote:
Hello,
I am trying to run a MD simulation on trehalose (glucose disaccharide)
in water. I obtained the PDB file from the URL:
http://www.rcsb.org/pdb/files/ligand/TRE_model.pdb . When I run pdb2gmx
on the PDB file:
pdb2gmx -f TRE_model.pdb -o TRE_model.gro -v
I chose force
Hello,
I am trying to run a MD simulation on trehalose (glucose disaccharide) in
water. I obtained the PDB file from the URL:
http://www.rcsb.org/pdb/files/ligand/TRE_model.pdb . When I run pdb2gmx on
the PDB file:
pdb2gmx -f TRE_model.pdb -o TRE_model.gro -v
I chose force field 5 (OPLS) from
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