On 10/25/19 7:43 AM, Amit Jaiswal wrote:
Dear Jorden,
I tried the simulation by changing the residue number in .itp file but
it still goes out of the box during NVT. As Justin mentioned that the
naming of the residue is irrelevant, so I guess either I am doing some
minor mistake in
I had
Dear Jorden,I tried the simulation by changing the residue number in .itp file but it still goes out of the box during NVT. As Justin mentioned that the naming of the residue is irrelevant, so I guess either I am doing some minor mistake in topology naming. So, I have included the order of
On 10/22/19 12:04 AM, Amit Jaiswal wrote:
Dear Jorden,
Thanks for your reply. As you have suggested, i found there is a
mismatch of the atom number in the zn.itp file and the .gro file. I
have included few residues of .gro file for your convenience.
What i understand is that I have to
Dear Amit,
Yes, you need to correct the atom number in the "zn.itp" file in your case.
>From your co-ordinate file, it is clear that in order to restrain Zn atom
you need to put restraint potential on atom number corresponding to Zn atom
which is 4265 in your case instead of 2220. I think this
Dear Jorden, Thanks for your reply. As you have suggested, i found there is a mismatch of the atom number in the zn.itp file and the .gro file. I have included few residues of .gro file for your convenience. What i understand is that I have to rename the zn.itp file with residue no. 4265 and not
Dear Amit,
Your files look correct to me. If "2220" atom in your coordinate file is
the "Zn" atom, it should not be displaced because, from your mdp file and
topology setting you have restrained all the heavy atoms of Protein, Nad
and Zn. I don't understand why it is happening. Even the
Dear Jorden, Many thanks for your reply. I have mentioned the files below for you to have a look. Once again thanks for your time. NVT.mdp:title = Protein-ligand complex NVT equilibrationdefine = -DPOSRES -DPOSRES_LIG ; position restrain the protein and ligand; Run parametersintegrator = md ;
On 10/14/19 11:54 PM, ISHRAT JAHAN wrote:
Go through at the following link. Hope it will resolve the issue-
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html
Please update your bookmarks. That site is wildly outdated and will be
taken offline
Go through at the following link. Hope it will resolve the issue-
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html
On Tue, Oct 15, 2019 at 7:26 AM Jorden Cabal wrote:
> Dear Amit,
> During equilibration you add positional restraint for protein, notice
Dear Amit,
During equilibration you add positional restraint for protein, notice that
you have added positional restraint for Zn ion, nad and protein. It should
not happen if you have taken the default values while generating the
positional restraints in gromacs. However I would like to look to
Dear Jorden, Many thanks for your suggestions. I solved the index file problem as I created two groups namely Protein_Zn_NAD and the other being Na_Water. But when i ran NVT equilibration, the Zn ion again got displaced far away from its original position. I cannot figure out how can i constrain
Dear Amit,
Please check if the Zn ion is included in both the groups declared for
temperature coupling. If you notice that it is is included, you can simply
create a group of all the atoms which is not in "Protein_NAD" group. You
can do this by using "!group_number" as far as I remember. Then try
Hello Everyone, I have solved this problem. However,i would like to ask how can I make an index file for Temperature Coupling for Protein_Zn_Ligand? When i tried to make the index group for the Protein_Zn_Ligand and I got the following error. Is the nvt simulation correct if i don't add Zn to the
Dear Jorden, Thanks for reply. I followed your suggestions and i got an error as follows: Command line: gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr Ignoring obsolete mdp entry 'title'Setting the LD random seed to 1403244422Generated 100032 of the 100128
Hi Amit,
The metal ion needs to be treated very very carefully so as to maintain
their co-ordination state with the nearby atoms of protein.
To do this, one needs to generate the parameter separately for the complex
formed by the metal ion with the protein residues because due to presence
of metal
Hello Everyone,
Would you please let me know what should we do when the zinc ion gets displaced
during simulation of a Protein-Zn-Ligand complex? What are the possible options
one can perform under such conditions? If possible, please mention the steps
needed to be performed briefly as i am
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