Dear Emran Heshmati,
I can not see any graph? Did you attach it. Please verify.
Thank you
On Fri, Mar 27, 2020 at 6:21 PM Emran Heshmati wrote:
> I am working on a protein consisting 2 chains. After performing regular MD
> simulation and analysis the outputs, I got unexpecter rmsd, as shown in
> 391THR OT1 4263 4.599 5.012 3.355
> 391THR OT2 4264 4.496 5.082 3.173
> 392ZN ZN 4265 7.278 6.612 5.838
> 393NAD PA 4266 6.217 7.359 2.802
> 393NAD O1A 4267 6.090 7.410 2.863
> 393NAD O2A 4268 6.337 7.451 2.808
> 393NAD O5B 4269 6.185 7.331 2.647
> 393NAD C5B 4270 6
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
ude topology for ions*
> *#include "./charmm36-mar2019.ff/ions.itp"*
>
>
> *[ system ]*
> *; Name*
> *Protein in water*
>
> *[ molecules ]*
> *; Compound #mols*
> *Protein_chain_A 1*
> *ZN 1*
> *NAD 1*
> *SOL 12908*
> *NA 4*
>
> With kind re
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
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
Hi Anupama,
I understand your question. But I wonder why do you want all the explicit
water molecules within 5 Angstrom of your protein surface? That would be
meaningless until and unless you are intending to find the conserved water
molecules near the surface of protein. I don't understand your
n Tue, Aug 20, 2019 at 9:25 PM Justin Lemkul wrote:
>
>
> On 8/20/19 5:21 AM, Jorden Cabal wrote:
> > Hi Justin,
> > Thank you for your response. In my case the cost of increasing simulation
> > box is very large. I have already tried it by keeping distance betwee
Hi Sumedha,
I think you are using the default value of -len (i.e Mean distance for
histogramming) in the command which is 0.1. If you data points contains
distance values which has larger mean than this, histogramming for those
values will not be calculated. For conformation, you can check the
, 2019 at 8:00 PM Justin Lemkul wrote:
>
>
> On 8/19/19 12:39 AM, Jorden Cabal wrote:
> > Dear Users,
> > I am trying to perform simulation of a very large and complex system and
> > which requires me to make the simulation box rectangular cube instead
> (box
> > d
I think the answer is not so straightforward. It depends upon a lot of
things, but I would say that the parameters derived using QM is better. If
you do not have any other options you can still use PRODRG server but even
in that case, I find many people using the docked (or bound) conformation
of
Dear Users,
I am trying to perform simulation of a very large and complex system and
which requires me to make the simulation box rectangular cube instead (box
dimension 24.5 nm * 12.5 nm * 12.3 nm) of perfect cuboid in order to
minimize the number of atoms present in the system.
I am facing the
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