Ho THANKS
MANY THANKS
I'm sorry, I'm new to Gromacs, and finally got it. Thank you very much.
Hagit.
2012/5/2 Mark Abraham
> On 2/05/2012 8:55 PM, Hagit G wrote:
>
> Hi gmx users,
>
>
> Well, I saw this question but the answer was not understood.
> I'm trying to work with the file 1PPB.pdb.
On 2/05/2012 8:55 PM, Hagit G wrote:
Hi gmx users,
Well, I saw this question but the answer was not understood.
I'm trying to work with the file 1PPB.pdb. There are 2 chains
connected with a disulfide bond. Gromacs automatically adds H atoms.
Although the disulfide bond is there, Gromacs ignore
On 5/2/12 6:55 AM, Hagit G wrote:
Hi gmx users,
Well, I saw this question but the answer was not understood.
I'm trying to work with the file 1PPB.pdb. There are 2 chains connected with a
disulfide bond. Gromacs automatically adds H atoms.
Although the disulfide bond is there, Gromacs ignore
Hi gmx users,
Well, I saw this question but the answer was not understood.
I'm trying to work with the file 1PPB.pdb. There are 2 chains connected
with a disulfide bond. Gromacs automatically adds H atoms.
Although the disulfide bond is there, Gromacs ignore it because *each
cystein is on a diffe
Dear All,
Just to confirm what Justin said, my MD worked flawlessly with his
ffG43a1p files.
The only issue was that I had to change my pr.mdp and md.mdp files,
following a suggestion I found here: I changed the T coupling groups
to "Protein" and "Non-Protein" (I am using the same temperature for
t
Dear All,
In working with Nelson on his problem (below), I made some headway into figuring
out what is going on with the ffG43a1p force field files. I know a few others
have asked questions about it across this list, so I thought I would send this
out to everyone.
By modifying a few entries in t
Hi Maik,
Thanks for the warning and the tip, I have already donwloaded and will
read that paper today, it seems to be what I need.
I have been working with MD for some 6 months now (I know that's not
much), and have had the help of some knowledgeable people, but they
are unavailable right now.
I ju
Hi
First of all, I think its dangerous to perform MD simulations without
any knowledge about the details of MD.
So the first suggestion is: Inform yourself (by reading the manual)
about MD and GROMACS. Using a black box is, maybe, often done, but
surely not the best way to go.
Before starting
Nelson,
A long while back, a member of our lab contemplated simulating a phosphorylated
protein, but ran into some issues as well. I tried to help him by editing the
ffG43a1p files, and I seem to remember making some headway. If you'd like, you
can send me your .pdb file (off-list) and I'll test
Hi Justin,
Thanks for the reply.
Yes, I used PRODRG Beta. Thanks for the heads up about the charges.
The error I got using ffG43a1 was this:
>Fatal error:
> wrong format in input file ffG43a1p.hdb on line
>2 7 OW
which was also described here:
http://www.gromacs.org/pipermail/gm
Quoting Nelson Cotrim <[EMAIL PROTECTED]>:
> Hi gmx users,
> I am rather new to MD, Linux environment and almost everything related
> to it. I am a geneticist working on mutations, so please, keep it
> simple :)
> This may be trivial and there may be an answer on the list already,
> but I do not e
Hi gmx users,
I am rather new to MD, Linux environment and almost everything related
to it. I am a geneticist working on mutations, so please, keep it
simple :)
This may be trivial and there may be an answer on the list already,
but I do not even know how to search for it - the way I tried did not
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