Please don't reply to the entire digest; cut out only the relevant parts.
On 8/8/17 2:37 AM, G R wrote:
Hi,
Thank you for your answer. yes, I know that I should make my own
forcefield in my working directory, and I made this forcefield, but when I
use x2top to generate itp file, gro
Im working on simulating a CYP2D6 with its cofactors (heme ) with GROMACS.
When I run pdb2gmx, using CHARMM27 FF, I had no error.
After looking in the literature, I found their corresponding
parameters: I added the following fields in CHARMM file ffbonded.itp
[
bondtypes ]
;
i j func b0 kb
SG
FE 1
Thank you for your help!
Best regards,
Mahsa
On Mon, Aug 7, 2017 at 4:35 PM, Justin Lemkul wrote:
>
>
> On 8/6/17 8:35 PM, Mahsa E wrote:
>
>> Hello Justin,
>>
>> Thank you so much for your reply!
>>
>> I followed what you suggested. Please correct me if I misunderstood;
>>
>> 1- I used acpype
Hi All,
I want to calculate interaction between 2 energy groups, which were not
defined during the run. So I want to rerun and include both the energy
groups while rerunning. This can be easily done by again assembling .tpr
file from .gro, .top and .cpt file by grompp, but I donot have the .gro and
Hi,
I am trying to run a protein/water simulation using a new computer (Ryzen
1700X, Nvidia GTX 1070 running Ubuntu 17.04). I compiled GROMACS 2016.3 with
gcc-5 (CUDA 8.0 complained that it only supports up to version 5) and
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON, otherwise defaul
Dear Sir,
Here is my part of the ligand energy.
*Energies (kJ/mol)*
* Bond Angle Proper Dih.
Ryckaert-Bell.LJ-14*
3.27203e+019.31977e+012.74737e+004.46079e+012.42598e+01
*Coulomb-14LJ (SR) Disper. corr. Coulom
On 8/8/17 1:06 PM, Sorour Hasani wrote:
Im working on simulating a CYP2D6 with its cofactors (heme ) with GROMACS.
When I run pdb2gmx, using CHARMM27 FF, I had no error.
After looking in the literature, I found their corresponding
parameters: I added the following fields in CHARMM file ffbonded
On 8/8/17 4:03 PM, Tushar Ranjan Moharana wrote:
Hi All,
I want to calculate interaction between 2 energy groups, which were not
defined during the run. So I want to rerun and include both the energy
groups while rerunning. This can be easily done by again assembling .tpr
file from .gro, .top a
On 8/8/17 7:26 PM, Mohammad Zahidul Hossain Khan wrote:
Dear Sir,
Here is my part of the ligand energy.
*Energies (kJ/mol)*
* Bond Angle Proper Dih.
Ryckaert-Bell.LJ-14*
3.27203e+019.31977e+012.74737e+004.46079e+012.42598e+01
Hi everyone,
I am trying to calculate the binding free energy between protein and ligand
by using MM/PBSA. I included all the .itp files. But when run the command,
am getting an error saying "NO XTC" Could someone help me, what would be
wrong, why such error occurs. i have pasted the error messag
can you please paste your command line here?
we can judge where you are wrong
On Aug 9, 2017 12:50 PM, "Kingsley Theras Primus Dass ." <
105726...@gms.tcu.edu.tw> wrote:
Hi everyone,
I am trying to calculate the binding free energy between protein and ligand
by using MM/PBSA. I included all the
Hi,
How to get good (and fast) performance from mdrun through available 8
logical CPU cores?
When I gave,
gmx mdrun -ntmpi 2 -ntomp 4 -v -deffnm eq
It seems to be slow, much slower than
gmx mdrun -v -deffnm eq.
Can anyone help?
Thanks,
Vidya R
--
Gromacs Users mailing list
* Please search
sure
the below is my command line
qsub /home/hauren32/Desktop/work/MM_PBSA_2.0/GMXPBSAtool/gmxpbsa0-1_TEST.pbs
and the files i have are
1. npt.xtc
2.npt.tpr
2.index.ndx
3.topol.top
4. gdp.itp
5.protein.itp
2017-08-09 12:22 GMT+08:00 Amir Zeb :
> can you please paste your command line her
Hi,
You need to try all the possibilities and find out what combinations gives
you the best. Further, I don't think you can achieve anything good with 8
logical processors for 'medium' protein or MD system.
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Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Supp
It would be better if you follow this link for mmpbsa calculations
http://rashmikumari.github.io/g_mmpbsa/
good luck
On Aug 9, 2017 1:35 PM, "Kingsley Theras Primus Dass ." <
105726...@gms.tcu.edu.tw> wrote:
> sure
> the below is my command line
> qsub /home/hauren32/Desktop/work/MM_PBSA_2.
Please refer to our mailing list
https://groups.google.com/forum/m/?utm_medium=email&utm_source=footer#!forum/gmxpbsa
Best
Messaggio originale
Oggetto: Re: [gmx-users] MM/PBSA
Da: "Kingsley Theras Primus Dass ." <105726...@gms.tcu.edu.tw>
A: gmx-us...@gromacs.org
CC:
sure
Thanks a lot Justin.
On Wed, Aug 9, 2017 at 1:33 AM, Tushar Ranjan Moharana <
tusharranjanmohar...@gmail.com> wrote:
> Hi All,
> I want to calculate interaction between 2 energy groups, which were not
> defined during the run. So I want to rerun and include both the energy
> groups while rerunnin
On Wed, Aug 9, 2017 at 1:04 AM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
> Send gromacs.org_gmx-users mailing list submissions to
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