no grompp not gives any warning neither i have used -maxwarn option.
On Mon, Sep 11, 2017 at 5:26 PM, Justin Lemkul wrote:
>
>
> On 9/11/17 2:43 AM, ISHRAT JAHAN wrote:
>
>> how can i check whether the structure is whole or not in .tpr file? After
>> trjconv whole stage i got
On 9/11/17 2:43 AM, ISHRAT JAHAN wrote:
how can i check whether the structure is whole or not in .tpr file? After
trjconv whole stage i got broken structure.
This is beyond just a "broken" structure. No amount of PBC manipulation
will fix this; it's as if the topology wasn't sound and you
Here i am providing you the link of protein structure
https://we.tl/X4yEyZq2aR
On Sun, Sep 10, 2017 at 8:59 PM, Justin Lemkul wrote:
>
>
> On 9/10/17 3:27 AM, ISHRAT JAHAN wrote:
>
>> Dear Justin
>> I have used all the commands given in the link provided by you but unable
>> to
how can i check whether the structure is whole or not in .tpr file? After
trjconv whole stage i got broken structure.
On Sun, Sep 10, 2017 at 9:00 PM, Mark Abraham
wrote:
> Hi,
>
> You seem to reporting that your system isn't whole. Is it whole after the
> trjconv
Hi,
You seem to reporting that your system isn't whole. Is it whole after the
trjconv -whole stage? Is the structure in that .tpr whole?
Mark
On Sun, Sep 10, 2017 at 9:27 AM ISHRAT JAHAN wrote:
> Dear Justin
> I have used all the commands given in the link provided by you
On 9/10/17 3:27 AM, ISHRAT JAHAN wrote:
Dear Justin
I have used all the commands given in the link provided by you but unable
to get the solution.
commands used by me are-
trjconv -f prtn_full.xtc -s prtn_md.tpr -o prtn_md_whole.xtc -pbc whole -n
prtn_drg.ndx
trjconv -f prtn_md_whole.xtc -s
Dear Justin
I have used all the commands given in the link provided by you but unable
to get the solution.
commands used by me are-
trjconv -f prtn_full.xtc -s prtn_md.tpr -o prtn_md_whole.xtc -pbc whole -n
prtn_drg.ndx
trjconv -f prtn_md_whole.xtc -s prtn_md.tpr -o prtn_md_cluster.xtc -pbc
On 9/9/17 10:12 AM, ISHRAT JAHAN wrote:
Actually my final .gro file is totally broken into smaller parts when i
load it in vmd, for this what will i do?
Again, everything you need is in the link I provided.
-Justin
On Sat, Sep 9, 2017 at 7:36 PM, Justin Lemkul wrote:
Actually my final .gro file is totally broken into smaller parts when i
load it in vmd, for this what will i do?
On Sat, Sep 9, 2017 at 7:36 PM, Justin Lemkul wrote:
>
>
> On 9/9/17 10:05 AM, ISHRAT JAHAN wrote:
>
>> Dear Justin
>> commands which i have used are given belown-
On 9/9/17 10:05 AM, ISHRAT JAHAN wrote:
Dear Justin
commands which i have used are given belown-
gmx trjconv -f protein_out.xtc -s protein_md.tpr -o protein_nojump.xtc -pbc
nojump
gmx trjconv -f protein_nojump.xtc -s protein_md.tpr -o protein_cluster.xtc
-pbc cluster
gmx trjconv -f
Dear Justin
commands which i have used are given belown-
gmx trjconv -f protein_out.xtc -s protein_md.tpr -o protein_nojump.xtc -pbc
nojump
gmx trjconv -f protein_nojump.xtc -s protein_md.tpr -o protein_cluster.xtc
-pbc cluster
gmx trjconv -f protein_cluster.xtc -s protein_md.tpr -o
On 9/9/17 1:50 AM, ISHRAT JAHAN wrote:
Dear all,
I have done 100ns md simulation of protein with drug using amber99sb.ff
with gromacs-5.1.4 version. After simulation i found my protein broken into
smaller parts in .gro file but when i load the final xtc file to pr.gro
molecule does not break.
Dear all,
I have done 100ns md simulation of protein with drug using amber99sb.ff
with gromacs-5.1.4 version. After simulation i found my protein broken into
smaller parts in .gro file but when i load the final xtc file to pr.gro
molecule does not break. I have applied -pbc nojump ,cluster and
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