blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } No I meant my newtrj.xtc file In fact I watched my trajectory
file before and it was ok
Sent from Yahoo Mail for iPhone
On F
On 11/10/17 11:22 AM, farial tavakoli wrote:
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Then I ignore that i cant visualize the protein motion in vmd
and go on the l
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Then I ignore that i cant visualize the protein motion in vmd
and go on the left steps of the results quality assuranc?
Sent
On 11/10/17 11:02 AM, farial tavakoli wrote:
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } so how come i bring the .gro and newtrj.xtc files in the vmd ,
my protein does
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } so how come i bring the .gro and newtrj.xtc files in the vmd ,
my protein doesnt move at all? I think , it is because of the .gr
On 11/10/17 10:35 AM, farial tavakoli wrote:
Dear Justin
Thank you for replying
This is my input xtc file :
gmx check -f md_0_1.xtc
Checking file md_0_1.xtc
Reading frame 0 time 0.000
# Atoms 49582
Precision 0.001 (nm)
Last frame 1000 time 1.000
Item #frames Tim
>
> From: Justin Lemkul
> To: gmx-us...@gromacs.org
> Sent: Wednesday, 4 October 2017, 15:19:38
> Subject: Re: [gmx-users] peptide ligand
>
>
>
> On 10/3/17 1:51 PM, farial tavakoli wrote:
>> blockquote, div.yahoo_quoted { margin-left: 0 !importan
bably lost track of what you (think you) are doing.
-Justin
From: Justin Lemkul
To: gmx-us...@gromacs.org
Sent: Wednesday, 4 October 2017, 15:19:38
Subject: Re: [gmx-users] peptide ligand
On 10/3/17 1:51 PM, farial tavakoli wrote:
blockquote, div.yahoo_quoted { marg
I entered,
noticed I had md.log file not npt.log. and it runs to 272000 steps . Why?Would
you please help me how come it runs this way?
From: Justin Lemkul
To: gmx-us...@gromacs.org
Sent: Wednesday, 4 October 2017, 15:19:38
Subject: Re: [gmx-users] peptide ligand
On 10/3/17 1
Dear Justin
Thank you so much for all of your help
best
Farial
From: Justin Lemkul
To: gmx-us...@gromacs.org
Sent: Wednesday, 4 October 2017, 15:19:38
Subject: Re: [gmx-users] peptide ligand
On 10/3/17 1:51 PM, farial tavakoli wrote:
> blockquote, div.yahoo_quoted { mar
On 10/3/17 1:51 PM, farial tavakoli wrote:
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Because in tuturial , energygroups = protein JZ4So I think ,I
have to seperate m
On 10/3/17 1:46 PM, farial tavakoli wrote:
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Oh I am sorry. Yes I am trying to run md on my protein peptide
complex. At first
;> creating topology for each of them separately ?
>>>
>>
>> As long as the protein and peptide ligand are denoted as being in
>> separate chains (different chain ID or use of TER in the PDB file), then
>> pdb2gmx will do everything for you.
>>
>> -Justin
>&
in the PDB file), then
>> pdb2gmx will do everything for you.
>>
>> -Justin
>>
>>>
>>>
>>>
>>> *From:* Justin Lemkul
>>> *To:* gmx-us...@gromacs.org; far
e chains (different chain ID or use of TER in the PDB file), then
pdb2gmx will do everything for you.
-Justin
*From:* Justin Lemkul
*To:* gmx-us...@gromacs.org; farial tavakoli
*Sent:* Tuesday, 3 October 2017, 16:35
enoted as being in
> separate chains (different chain ID or use of TER in the PDB file), then
> pdb2gmx will do everything for you.
>
> -Justin
>
>>
>>
>>
>> *From:* Justin Lemkul
>
.
-Justin
*From:* Justin Lemkul
*To:* gmx-us...@gromacs.org; farial tavakoli
*Sent:* Tuesday, 3 October 2017, 16:35:49
*Subject:* Re: [gmx-users] peptide ligand
On 10/3/17 4:26 AM, farial tavakoli wrote:
Dear GROMACS users
I need to run a MD on my Protein-peptide liga
n
pdb2gmx will do everything for you.
-Justin
>
>
>
> *From:* Justin Lemkul
> *To:* gmx-us...@gromacs.org; farial tavakoli
>
> *Sent:* Tuesday, 3 October 2017, 16:35:49
> *Subject:* Re: [gmx-use
:35:49
*Subject:* Re: [gmx-users] peptide ligand
On 10/3/17 4:26 AM, farial tavakoli wrote:
> Dear GROMACS users
> I need to run a MD on my Protein-peptide ligand complex in GROMACS.
I generated my ligand topology by gromose96 54a7 ff ( [moleculetypes]
was Protein_chain_B) and converted
On 10/3/17 4:26 AM, farial tavakoli wrote:
Dear GROMACS users
I need to run a MD on my Protein-peptide ligand complex in GROMACS. I generated
my ligand topology by gromose96 54a7 ff ( [moleculetypes] was Protein_chain_B)
and converted it to .itp file to string it in Protein.top file, then
Dear GROMACS users
I need to run a MD on my Protein-peptide ligand complex in GROMACS. I generated
my ligand topology by gromose96 54a7 ff ( [moleculetypes] was Protein_chain_B)
and converted it to .itp file to string it in Protein.top file, then, added
Protein_chain_B in [ molecules ] directive
Dear GMX users
I want to generate a topology for my peptide ligand, but I dont know if I can
use "gmx pdb2gmx -f peptide ligand-protein complex.pdb -o peptide
ligand-protein complex.gro -water spce -ignh" ?would you please advice me that
how can I generate a peptide ligand topology file? I think
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