Thank you sir.
On Fri, Sep 27, 2013 at 11:47 AM, Tsjerk Wassenaar wrote:
> Yes.
>
> Cheers,
>
> Tsjerk
>
>
> On Fri, Sep 27, 2013 at 7:51 AM, Venkat Reddy wrote:
>
> > Thanks for the quick reply sir.
> > So, does it mean I can apply "trjcat" on the processed xtc files???
> >
> >
> > On Thu, Sep
Dear all gmx users
I would like to calculate pc loadings for various integrated factors in the
form of following sample table:
Integrated factorsPC1PC2PC3 PC4PC5PC6PC7PC8 PC9PC10Total nonpolar surface
area0.60 -0.07-0.76-0.11-0.060.11 0.05-0.160.06-0.02Chain exposed area 0.92
-0.14-0.050.12 0.230.
Dear Justin,
sorry for the late answer and acknowledgements... Please see below my
comments.
Anna
__
Anna Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via Giovanni Paolo II, 132
84084 Fisciano (SA)
Ita
Hi Pratibha,
The table is all garbled, and your description insufficiently clear for us
to form a mental picture of what you want, what you've tried to get that,
where it goes wrong, or where you get stuck, and how we can help you on the
right track again.
Cheers,
Tsjerk
On Fri, Sep 27, 2013 a
On 9/27/13 8:18 AM, Anna Marabotti wrote:
Dear Justin,
sorry for the late answer and acknowledgements... Please see below my
comments.
Anna
__
Anna Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via G
On 26 Sep, 2013, at 19:50, Justin Lemkul wrote:
> On 9/26/13 10:47 PM, Christopher Neale wrote:
>> Dear Karthi:
>>
>> As far as I am aware, there is no OPLSAA lipid force field. I have used
>> Berger lipids with OPLSAA protein
>> ( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but t
Hello Gromacs users,
I am the beginner in Gromacs. I want to simulate ionomer in water. I could not
find a pdb file for my case, and I tried to draw the ionomer in Avogadro
software and generated the pdb file. However, gmx cannot find my residue names.
I added my residue name to residuetypes.da
On 9/27/13 2:34 PM, Ehsan Sadeghi wrote:
Hello Gromacs users,
I am the beginner in Gromacs. I want to simulate ionomer in water. I could
not find a pdb file for my case, and I tried to draw the ionomer in Avogadro
software and generated the pdb file. However, gmx cannot find my residue
names.
Many thanks Justin.
Here is my .pdb file:
ATOM 1 C LIG 1 -10.450 5.214 -1.717 1.00 0.00 C
ATOM 2 C LIG 1 -8.424 5.477 -1.030 1.00 0.00 C
ATOM 3 C LIG 1 -6.603 5.864 -0.166 1.00 0.00 C
ATOM 4
On 9/27/13 3:17 PM, Ehsan Sadeghi wrote:
Many thanks Justin.
Here is my .pdb file:
ATOM 1 C LIG 1 -10.450 5.214 -1.717 1.00 0.00 C
ATOM 2 C LIG 1 -8.424 5.477 -1.030 1.00 0.00 C
ATOM 3 C LIG 1 -6.603 5.864 -0.1
Hi,
I just added this to the existing .rtp file in gromos
[ LIG ]
[ atoms ]
C C 0.000 0
F F 0.000 0
[ SCH ]
[ atoms ]
OOM 0.000 0
C C 0.000 0
O O 0.000 0
F F 0.000 0
S S 0.000 0
H
On 9/27/13 4:18 PM, Ehsan Sadeghi wrote:
Hi,
I just added this to the existing .rtp file in gromos
[ LIG ]
[ atoms ]
C C 0.000 0
F F 0.000 0
[ SCH ]
[ atoms ]
OOM 0.000 0
C C 0.000 0
O O 0.000 0
F F
Thanks Chris.
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Christopher Neale
Sent: Thursday, September 26, 2013 7:47 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Membrane simulation with OPLS ff.
Dear Karthi:
As far as I
Thanks Justin.
I try to modify my file based on your comments.
- Original Message -
From: "Justin Lemkul"
To: "Discussion list for GROMACS users"
Sent: Friday, September 27, 2013 1:24:44 PM
Subject: Re: [gmx-users] ionomer topolgy
On 9/27/13 4:18 PM, Ehsan Sadeghi wrote:
> Hi,
>
> I
Thanks Justin.
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Justin Lemkul
Sent: Thursday, September 26, 2013 7:51 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Membrane simulation with OPLS ff.
On 9/26/13
Hello,
I revised my pdb and rtp files. I still receive similar error message.
Here are the new files:
.pdb:
ATOM 1 C1LIG 1 -10.450 5.214 -1.717 1.00 0.00
C
ATOM 2 C2LIG 1 -8.424 5.477 -1.030 1.00 0.00
C
ATOM 3 C3
On 9/27/13 5:53 PM, Ehsan Sadeghi wrote:
Hello,
I revised my pdb and rtp files. I still receive similar error message.
Whatever modifications you're making probably aren't being done in the right
files. You haven't yet responded to my question about which force field you're
using and whe
Thanks for your prompt response. I made the modifications on the aminoacids.rtp
file in Gromacs/gromacs-4.6.3/share/top/gromos53a6.ff.
I did not modify any force field. I thought I still can use the default force
field in gromos; isn't it right?
Here is the output from pdb2gmx. Thank you for you
On 9/27/13 8:43 PM, Ehsan Sadeghi wrote:
Thanks for your prompt response. I made the modifications on the aminoacids.rtp
file in Gromacs/gromacs-4.6.3/share/top/gromos53a6.ff.
I did not modify any force field. I thought I still can use the default force
field in gromos; isn't it right?
Yes
Dear Chris,
Thank you for your reply. I defined a new virtual atomtype (type D) with
LJ sigma 1.72A ( 2*0.7+1.72=3.12, which is sigma of the oxygen) and
played a bit with epsilon till the new LJ repulsion was able to prevent
the build up of a huge force on the oxygen while interacting with
dim
Dear all users
I would like to calculate pc loadings for various integrated factors in the
form of following sample table:
Integrated Factors
PC1
PC2
PC3
PC4
PC5
PC6
PC7
PC8
PC9
PC10
Total non polar surface area
0.60
-0.07
-0.76
-0.11
0.08
0.05
-0.16
0.08
-0.01
0.02
Native
Hi Prathiba,
I think you should have a look at the "Functional Mode Analysis" method
from Bert de Groot's lab.
Cheers,
Tsjerk
On Sat, Sep 28, 2013 at 8:13 AM, pratibha kapoor
wrote:
> Dear all users
>
> I would like to calculate pc loadings for various integrated factors in the
> form of foll
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