leila karami wrote:
Dear Justin
Is there any way for this problem?
Please keep Tsjerk's comments
(http://lists.gromacs.org/pipermail/gmx-users/2010-October/054938.html) in mind.
If the calcium coordination complex plays only a minor structural role, you
can probably justify using distan
Dear Justin
Is there any way for this problem?
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leila karami wrote:
Dear Justin
thanks for your attention
in my case calcium ion is bonded to 4 oxygen atoms of C=O group of
protein. yes, Calcium ions are present in nearly all the force fields in
Gromacs. but there are only parameters in * nb.itp and not in * bon.itp.
how to obtain these
Dear Justin
thanks for your attention
in my case calcium ion is bonded to 4 oxygen atoms of C=O group of protein.
yes, Calcium ions are present in nearly all the force fields in Gromacs. but
there are only parameters in * nb.itp and not in * bon.itp. how to obtain
these new parameters for my case
Hi,
Do mind that calcium binding may involve (quantum) effects that are ill
captured by classical force fields. If the binding site plays a central role
in your research question, this may be problematic.
Cheers,
Tsjerk
On Oct 16, 2010 2:34 PM, "Justin A. Lemkul" wrote:
leila karami wrote: >
leila karami wrote:
Dear mohsen ramezanpour/ /
yes. calcium is a typical ligand in my pdb file.I used PRODRG server to make topology file but
ERRDRG> Too many atoms in this molecule (should be <=300).
PRODRG> Program terminated unsuccessfully, sorry!
There is no need to invoke PRODRG fo
Dear Leila
Yes,I think so
please read the article who I pointed,It can help you
On Sat, Oct 16, 2010 at 12:16 PM, leila karami wrote:
> Dear mohsen ramezanpour
>
>
> my pdb file has 3000atoms (protein) + 1 atom (calcium).
>
> Should I separate ion from general pdb again?
>
>
>
>
> --
> gmx-users
Dear mohsen ramezanpour
my pdb file has 3000atoms (protein) + 1 atom (calcium).
Should I separate ion from general pdb again?
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Dear Leila
Ok,But you have to separate your ions from your general pdb
file(protein+ions) in the form of pdb,
in the other words you need to obtain the pdb files for your ions separately
and then paste it to PRODRG server.because your protein has more than 300
atoms alonly.
I hope it can help you
Dear mohsen ramezanpour* *
yes. calcium is a typical ligand in my pdb file.I used PRODRG server
to make topology file but
ERRDRG> Too many atoms in this molecule (should be <=300).
PRODRG> Program terminated unsuccessfully, sorry!
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Hi
I think it is a typical ligand in your pdb file.what do you think?
if it be a ligand you can use PRODRG server to make topology file for your
ligand and you must edit other files.
please read this article: "GROMACS Tutorial for Drug – Enzyme Complex"
best
mohsen
On Sat, Oct 16, 2010 at 11:32 AM
Hi gromacs users
I want to study simulation of a protein including calcium ion. Can I use
gromacs force fields?
any help will highly appreciated.
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