On 24/11/2011 8:16 PM, cuong nguyen wrote:
Dear,
I create a box of water with 10 MIBC molecules on two opposite surfaces.
then I used the command "grompp -f input_min.mdp -o min.tpr -c
box1.g96" to creat .tpr file before using the command "genion -s
min.tpr -o add.gro -nname Cl -pname NA -nn 2
On Thu, Nov 24, 2011 at 5:16 PM, cuong nguyen wrote:
> Dear,
> I create a box of water with 10 MIBC molecules on two opposite surfaces.
> then I used the command "grompp -f input_min.mdp -o min.tpr -c box1.g96" to
> creat .tpr file before using the command "genion -s min.tpr -o add.gro
> -nname Cl
Objet :* Re: Re : [gmx-users] Adding Ions
Justin A. Lemkul wrote:
>
>
> errabah fatima ezzahra wrote:
>> i added the NA using the genion
>>*
>>
>> genion -s em.tpr -o waterbox_ions.gro -np 6 , and i added the
NA to the topology file , subtracted
Objet : Re: Re : [gmx-users] Adding Ions
Justin A. Lemkul wrote:
>
>
> errabah fatima ezzahra wrote:
>> i added the NA using the genion
>> *
>>
>> genion -s em.tpr -o waterbox_ions.gro -np 6 , and i added the NA to
>>the topology file ,
Justin A. Lemkul wrote:
errabah fatima ezzahra wrote:
i added the NA using the genion
*
genion -s em.tpr -o waterbox_ions.gro -np 6 , and i added the NA
to the topology file , subtracted the water number by 6. tail
waterbox_ions.gro file have this
3567WW 3789 1.256
*De :* Justin A. Lemkul
*À :* Discussion list for GROMACS users
*Envoyé le :* Mercredi 13 Juillet 2011 13h05
*Objet :* Re: [gmx-users] Adding Ions
errabah fatima ezzahra wrote:
>
> Hi All,
>
>
> I have a peptide that has three positive charged amino a
De : Justin A. Lemkul
À : Discussion list for GROMACS users
Envoyé le : Mercredi 13 Juillet 2011 13h05
Objet : Re: [gmx-users] Adding Ions
errabah fatima ezzahra wrote:
>
> Hi All,
>
>
> I have a peptide that has three positive charged amino acids (LYS)
errabah fatima ezzahra wrote:
Hi All,
I have a peptide that has three positive charged amino acids (LYS) and
four negative charged amino acids (GLU) consequently it is a negative
peptide. is that right
Assuming typical protonation states, and further assuming that there are no
other un
simon sham wrote:
Hi,
I have tried to add NaCl into my system in the 4.5.1 version to balance
the total charge, and used OPLS forcefield.
In the topol file file, it has CL- but no NA+. However, when I ran
grompp_d, it gave me the following error message:
Program grompp_d, VERSION 4.5.1
Sour
Hi,
Make sure you do specify the explicit names of the topology and structure
file. in the mannual they omit the suffix of the file.
for the purpose of rigourism - this is the line i'm using:
genion -pname Na+ -nname Cl- -o file_ionized.gro -conc 0.2 -p
topol.top
On Tue, Nov 17, 2009
The problem I was facing earlier: in the force field files (I am ussing
ffG53a6) the ions are named NA+, CL-, for example, so with capital letters.
Genion will add to the topology the ions named by default Na or Cl, unless
you use the options -pname and/or -nname to name the ions. I do so and I
hav
Arden Perkins wrote:
I am an undergraduate student and I am still learning to use GROMACS.
When I add my ions to the solution (using genion) by the procedure
described in the funnel web spider tutorial the .gro and .top files do
not match. I tried subtracting solvent molecules but they still
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