On 3/11/14, 6:32 AM, Nidhi Katyal wrote:
Thanks Mark. Yes, my ligand.itp indeed has both [atomtypes] entry as well
as [molecule] entry. I have followed the following procedure to #include
while creating my first molecule:
Run pdb2gmx command.
Added #include "ligand.itp" after
#include "charmm27
Thanks Mark. Yes, my ligand.itp indeed has both [atomtypes] entry as well
as [molecule] entry. I have followed the following procedure to #include
while creating my first molecule:
Run pdb2gmx command.
Added #include "ligand.itp" after
#include "charmm27.ff/forcefield.itp"
but before
[ moleculetype
Probably you will see that your ligand.itp has an [atomtypes] entry as well
as a [molecule] entry, and the former cannot follow any instance of the
latter. Such an .itp file must be #included to create the first molecule.
You have your protein [molecule] above the #include "ligand.itp" at the
momen
To test swiss param parameters, I have generated *.pdb and *.itp files from
it. In the genbox command, I have used -ci *.pdb -nmol 2.
I have included *.itp in the topology as:
; Include Position restraint file
;#ifdef POSRES
;#include "posre.itp"
;#endif
;Include ligand topology
#include "ligand.
On 3/10/14, 8:21 AM, Nidhi Katyal wrote:
Thanks Justin. I would also like to know the reliability of parameters
generated using swiss param.
I have no personal experience with it. My rule is to never trust anything from
a black-box server without verifying it and assessing any information
Thanks Justin. I would also like to know the reliability of parameters
generated using swiss param.
On Mon, Mar 10, 2014 at 3:13 PM, Justin Lemkul wrote:
>
>
> On 3/10/14, 2:45 AM, Nidhi Katyal wrote:
>
>> Thank you Mark and Justin.
>> Now, I have carried out simulations using PME electrostatic
On 3/10/14, 2:45 AM, Nidhi Katyal wrote:
Thank you Mark and Justin.
Now, I have carried out simulations using PME electrostatics and using all other
parameters (except gromos 96 43a1 ff used) as suggested in
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
The p
Thank you Mark and Justin.
Now, I have carried out simulations using PME electrostatics and using all
other parameters (except gromos 96 43a1 ff used) as suggested in
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
The protein is not loosing its structure now. But
On 2/17/14, 4:16 AM, Nidhi Katyal wrote:
Dear all
I am trying to simulate a protein in 3 steps: energy minimization (using
em.mdp), position restraints (using pr.mdp) and final production run by NPT
ensemble (using full.mdp) at 300K
At this temperature, it is known by previous literature surv
Seems like you're using cut-off electrostatics, which would be a good way
of picking lottery numbers, and that's about all.
Mark
On Mon, Feb 17, 2014 at 10:16 AM, Nidhi Katyal wrote:
> Dear all
>
> I am trying to simulate a protein in 3 steps: energy minimization (using
> em.mdp), position rest
Dear all
I am trying to simulate a protein in 3 steps: energy minimization (using
em.mdp), position restraints (using pr.mdp) and final production run by NPT
ensemble (using full.mdp) at 300K
At this temperature, it is known by previous literature survey that protein
keeps its secondary structure
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