I am not getting the "ffoplsaanb.itp" file for lipid simulation.PLease
tell me how to locate the file.
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How could we add DPPC group (for 6400 atoms) in index file?I have gone
through the gromacs tutorial
(http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx) but
not getting exactly.
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Plea
Shall we use 'residuetypes.dat' file in 'grompp -f minim.mdp -c
system_solv_ions.gro -p topol.top -o em.tpr' command without creating
index file?
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How to change parameters of JZ4 topology (as given in tutorial).I think the
explaination is given in the article (
Practical Considerations for Building GROMOS-Compatible Small-Molecule
Topologies) which is not freely available.Please help me.
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htt
Will you please send me the basic tutorial in which I can find how to use
-n option in " grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr" command.
On Mon, Feb 6, 2012 at 5:17 PM, Justin A. Lemkul wrote:
>
>
> Anushree Tripathi wrote:
>
>> where should I use -
where should I use -n option in the command (i.e., grompp -f nvt.mdp -c
em.gro -p topol.top -o nvt.tpr).Please tell me.
On Mon, Feb 6, 2012 at 4:58 PM, Mark Abraham wrote:
> On 6/02/2012 8:28 PM, Anushree Tripathi wrote:
>
>> Inspite of having DPPC in index file,when I run the c
Inspite of having DPPC in index file,when I run the command ( i.e., grompp
-f nvt.mdp -c em.gro -p topol.top -o nvt.tpr ),I am getting the error:
Group DPPC not found in indexfile.
Maybe you have non-default goups in your .mdp file, while not using the
'-n' option of grompp.
In that case use the '
into a single .gro file
> and also merge all of the parameters (.itp) into a single top file.
>
> As Mark said, pay attention to all everything on this page:
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html
>
> On 2012
ilayer
> though? If not, what is your reason for having it in your system?
>
> Also the topol.top file does not contain coordinates at all, only the
> forcefield parameterization.
>
> On 2012-02-02 12:11:44PM +0530, Anushree Tripathi wrote:
> > Please suggest me the exact way
Please suggest me the exact way to include dppc coordinates in topol.top
file.
On Wed, Feb 1, 2012 at 5:06 PM, Mark Abraham wrote:
> On 1/02/2012 6:25 PM, Anushree Tripathi wrote:
>
> But in coordinate file(.pdb file) ,I am not getting the atoms which
> belongs to DPPC.
>
&g
On Wed, Feb 1, 2012 at 12:40 PM, Mark Abraham wrote:
> On 1/02/2012 6:04 PM, Anushree Tripathi wrote:
>
> When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is
> showing the following options:
> 0 System : 18379 atoms
> 1 Protein
When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is
showing the following options:
0 System : 18379 atoms
1 Protein : 11739 atoms
2 Protein-H : 9135 atoms
3 C-alpha : 1173 atoms
4 Backbone: 3519 atoms
5 MainC
I am using gromacs 4.5.3 version.When I run the command (i.e., make_ndx -f
em.gro -o index.ndx),It is not showing any option for DPPC group which I
want to include.Please tell me how could I merge or create this option for
proceeding to the next step of NVT simulation.
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I am using single CPU for this simulation.
On Tue, Jan 31, 2012 at 11:09 AM, Emanuel Birru wrote:
> ** **
>
> *From:* gmx-users-boun...@gromacs.org [mailto:
> gmx-users-boun...@gromacs.org] *On Behalf Of *Anushree Tripathi
> *Sent:* Tuesday, 31 January 2012 4:11 PM
> *To:* D
How could I define the group for DPPC ?
On Tue, Jan 31, 2012 at 11:57 AM, Mark Abraham wrote:
> On 31/01/2012 5:14 PM, Anushree Tripathi wrote:
>
> When I run the command (i.e., grompp -f nvt.mdp -c em.gro -p topol.top -n
> index.ndx -o nvt.tpr)for volume equilibration.
>
>
When I run the command (i.e., grompp -f nvt.mdp -c em.gro -p topol.top -n
index.ndx -o nvt.tpr)for volume equilibration.
I am getting the error:
Fatal error:
Group DPPC not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the '-n'
option of grompp.
In that cas
When I run the command (i.e., mdrun -v -deffnm em) for energy minimization.
I am getting the error:
There is no domain decomposition for 4 nodes that is compatible with the
given box and a minimum cell size of 4.07513 nm.
Please guide me.
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http:
I have used "mdrun -v deffnm em" command for energy minimization just after
running the command i.e., given below:
perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
But When I run the command which is given below:
Ek! No confout.gro at all!
Died at inflategro.pl line 81.
alongwith HW) in dppc128.pdb file?
On Mon, Jan 23, 2012 at 6:41 PM, Justin A. Lemkul wrote:
>
>
> Anushree Tripathi wrote:
>
>> I am going through the Justin Lemku tutorial for KALP15 in DPPC. I have
>> reached step three, when I try to generate a trp file for
I am going through the Justin Lemku tutorial for KALP15 in DPPC. I have
reached step three, when I try to generate a trp file for DPPC only by
means of :
grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
I get the following warning:
Fatal error:
Atomtype OW not found
Any idea as t
comb-rulegen-pairsfudgeLJfudgeQQ
11no1.01.0
#include "ffnonbonded.itp"
#include "ffbonded.itp"
#include "lipid.itp"
Let me know whether it is correct or not.
On Mon, Jan 23, 2012 at 12:17 PM, Mark Abraham wrote:
> On
*I am using gromacs 4.5.3 version and I am trying to follow the
tutorials. For ** starting I am following the *KALP15 in DPPC* **
tutorial(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html).
*I am not getting the point that is given below :
Ne
*I am using gromacs 4.5.3 version and I am trying to follow the
tutorials. For ** starting I am following the *KALP15 in DPPC* **
tutorial(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html).
** But I am unable to locate following files in the G
I m not getting the meaning of source of error mentioned in user
i.e.,"charge groups encompass too many atoms. Most charge groups should be
less than 4 atoms or less".Let me know the exact meaning of this source of
error.Reply me soon.
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While running the command for NVT equilibration,I am getting one warning
for nvt.mdp i.e., The sum of the two largest charge group radii(2.334343)
is larger than rlist (1.00).But it is working and generating nvt.tpr
when I am using -maxwarn option.should I avoid this warning.Otherwise what
to d
Yes I m using 4.0.7 version.so for that how could I change the name
accordingly.
On Sat, Nov 5, 2011 at 1:37 AM, Justin A. Lemkul wrote:
>
>
> Anushree Tripathi wrote:
>
>> when i run the given command i.e,
>>
>> grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.
I want to simulate membrane protein in vaccum so let me know which force
field i can use for it.
Also I m doing simulation for the same protein in liquid using OPLS force
field.Please tell me is it correct?
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when i run the given command i.e,
grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr
It is showing fatal error:No such molecule type NA.
How could I troubleshoot this problem?
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Plea
I have seen different articles on MD simulation in vaccum but i didn't get
the exact way for it.If u can tell me the exact way then i can proceed for
it fastly because I have to do it within certain time limit.
On Thu, Nov 3, 2011 at 11:43 PM, Mark Abraham wrote:
> On 4/11/2011 4:58 AM,
Let me know how to simulate a membrane protein in vaccum medium by using
gromacs commands.What are the basic differences in commands as well as
parameters used in liquid and vaccum medium? Please guide me.
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I m using gromacs 4.5.3 version and trying to simulate a protein in liquid
media but I found problem in eqilibration step especially when I give
following command:
mdrun -deffnm nvt
.After giving this command it is showing error,i.e.,
There is no domain decomposition for 4 nodes that is compatibl
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