U can do in Gromacs 4.6.
Check the alignment of Zn in your pdb file, I hope a gap (space) is
inserted before the Zn.
Good Luck.
*Cheers*
Khuraijam
On Sat, May 31, 2014 at 11:42 AM, elham tazikeh
wrote:
> Dear Users
> I simulated Zinc ion on human growth hormone protein by Gromacs 4.6
> and e
Dear Users
I simulated Zinc ion on human growth hormone protein by Gromacs 4.6
and encountered with this message:
there are not molculetype for Zn
this sentence means I can not simulate this system on Gromacs 4.6 and have
to install version 4.5 on my system or not?
regards
elham tazikeh
--
Grom
Hi,
While issuing the command g_kinetics, I got an error saying that "the
program should be complied with GNU scientific library. Please install the
library and reinstall Gromacs". Is there an option where I can compile only
this tool, as rest of the other gromacs tools are working fine.
Regards
Here is one more thing (hopefully last!): If you have 8 energy groups,
there are lot of cross terms as you see. Some of these cross terms have to
be described by specific tables for each of those pairs. However, many
other pairs do not need specific tables, so a general table.xvg (not
specified b
On 5/30/14, 11:51 AM, 라지브간디 wrote:
Dear justin,
Thank your for your clear answer.
The parameters are specifically written for CHARMM force field based on the
experimental results.
Particularly, charges and non-bonded interaction values for ligand molecule of
CO ( Carbon Monoxide) in Myogl
Dear justin,
Thank your for your clear answer.
The parameters are specifically written for CHARMM force field based on the
experimental results.
Particularly, charges and non-bonded interaction values for ligand molecule of
CO ( Carbon Monoxide) in Myoglobin are written in literature.
Sinc
Albert,
The list does accept attachments. please file a redmine issue instead
(here: http://redmine.gromacs.org/). Include your input files and log
outputs too.
Have you observed the same issue without GPUs too? Is the crash
reliably reproducible? Does it always happen in the same replica? Does
i
indeed it is now working with -center - sorry for not having tried it
before ;)
thank you very much Justin, helpful as always!!
Nicola
On Fri, May 30, 2014 at 2:29 PM, Justin Lemkul wrote:
>
>
> On 5/30/14, 6:32 AM, Nicola Staffolani wrote:
>
>> Dear gmx community,
>>
>> I have a layer of Au
On 5/30/14, 7:50 AM, Mahboobeh Eslami wrote:
hi
dear justin
A few months ago I asked you a question about LIE method.
According
to your guide, i wrote a new .mdp file that didn't use PME (I used RF)
and used following command for protein-ligand complex? and ligand-sol
simulations:
?mdrun -s n
On 5/30/14, 6:32 AM, Nicola Staffolani wrote:
Dear gmx community,
I have a layer of Au atoms to which a molecule is attached. After pdb2gmx,
when I create the box and put H2O molecules inside using editconf, since
the planar dimensions of the Au layer are big compared to the corresponding
dime
On 5/29/14, 10:13 PM, 라지브간디 wrote:
Dear Justin,
Thanks for your
reply.
I am not mixing up the parameter here.
What i am trying to do here
In order to reproduce the dipole moments of the CO, I have to
follow up the specific charges and non-bonded interaction values specified in
literatur
hi
dear justin
A few months ago I asked you a question about LIE method.
According
to your guide, i wrote a new .mdp file that didn't use PME (I used RF)
and used following command for protein-ligand complex? and ligand-sol
simulations:
?mdrun -s newtpr.tpr -rerun full20ns.xtc
?then I extract -
it is better to avoid rotation at this initial stage. if you
experience certain features in your finals PMFs which you cannot
explain, you will always be unsure where they arrive from. this hurts
your soul.
Dr. Vitaly V. Chaban
On Thu, May 29, 2014 at 9:41 PM, ANDRES ADOLFO ORTEGA GUERRERO
wr
>
Dear all,
I have some questions when calculating frequency dependent dielectric
constants throughg_dielectric.
1. After using " g_dipoles -corr mol " command to get the dipcorr.xvg, if I
uesd " g_dielectric " program, the error is as following.
Fatal error:
npar
Dear gmx community,
I have a layer of Au atoms to which a molecule is attached. After pdb2gmx,
when I create the box and put H2O molecules inside using editconf, since
the planar dimensions of the Au layer are big compared to the corresponding
dimensions of the molecule, I have decided that I want
Dear gmx community,
I have a layer of Au atoms to which a molecule is attached. After pdb2gmx,
when I create the box and put H2O molecules inside using editconf, since
the planar dimensions of the Au layer are big compared to the corresponding
dimensions of the molecule, I have decided that I want
Dear gmx community,
I have a layer of Au atoms to which a molecule is attached. After pdb2gmx,
when I create the box and put H2O molecules inside using editconf, since
the planar dimensions of the Au layer are big compared to the corresponding
dimensions of the molecule, I have decided that I want
Dear David,
Thanks for your reply.
I have other questions when calculating frequency dependent dielectric
constants through g_dielectric.
1. After using " g_dipoles -corr mol " command to get the dipcorr.xvg, if I
uesd " g_dielectric " program, the error is as following.
==
Yes. Three parameters are needed for nbfunc 2 in order to use the few
kernels that implement Buckingham; using a Buckingham-shaped table with
nbfunc 1 is not "using Buckingham" from the point of view of how many
parameters grompp will expect.
Mark
On May 30, 2014 8:19 AM, "Chetan Mahajan" wrote:
Thanks for you help.
best regards
Haiping Zhang
发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
代表 Mark Abraham
发送时间: 2014年5月29日 17:50
收件人: Discussion list for GROMACS users
主题: Re: [gmx-users] 答复: Welcome to the "gromacs.org_gmx-users" mailing li
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