i will try ... and will reply pack to u
On Thu, Jun 23, 2011 at 4:39 PM, Ramachandran G wrote:
> It is neutral.
>
> I tried sending the coordinates but it bounces. So i paste below the
> chromophore coordinates alone.
>64CRIH CB2 948 2.946 2.849 3.832
>64CRIH HB2 949 2.948
It is neutral.
I tried sending the coordinates but it bounces. So i paste below the
chromophore coordinates alone.
64CRIH CB2 948 2.946 2.849 3.832
64CRIH HB2 949 2.948 2.845 3.932
64CRIH CA2 950 2.827 2.790 3.770
64CRIHN2 951 2.795 2.778 3.639
Is is this for the neutral chromophore or protonated one ??
On Thu, Jun 23, 2011 at 4:29 PM, Ramachandran G wrote:
> yes!
>
>
> On Thu, Jun 23, 2011 at 12:26 AM, bharat gupta
> wrote:
>
>> these are in continuity I mean for the ffbonded.itp file
>>
>> On Thu, Jun 23, 2011 at 4:21 PM, Ramachandr
yes!
On Thu, Jun 23, 2011 at 12:26 AM, bharat gupta wrote:
> these are in continuity I mean for the ffbonded.itp file
>
> On Thu, Jun 23, 2011 at 4:21 PM, Ramachandran G wrote:
>
>> more parameters - ffbonded.itp
>> NBCT 10.1444294553.6
>> NBC10.1404334720.0
these are in continuity I mean for the ffbonded.itp file
On Thu, Jun 23, 2011 at 4:21 PM, Ramachandran G wrote:
> more parameters - ffbonded.itp
> NBCT 10.1444294553.6
> NBC10.1404334720.0
> C CC 10.1407343088.0
> CCCB 10.1474
more parameters - ffbonded.itp
NBCT 10.1444294553.6
NBC10.1404334720.0
C CC 10.1407343088.0
CCCB 10.1474468608.0
CB H2 10.1076129960.25
to aminoacids.hdb
1 1 HE2 CE2 CZ CD2
1 1
For ffbonded.itp, i added the following. (you need to be carefull here since
i cooked upto the force constants)
C CCCBCA9 180.0 4.309 1
NBCCC O 9 180.0 4.309 1 ;
NBCCCBCA9 180.0 4.309 1
NBCCCBH29 180.0
For the GFP chromophore i name residue as CRIH.
1. aminoacids.rtp
CB2 CB 0.019103 1
CA2 CC-0.026635 2
N2 NB-0.436463 3
C1 CC 0.302706 4
N3 NB-0.541478 5
C2 C 0.563844
ok sir..
On Thu, Jun 23, 2011 at 4:06 PM, Ramachandran G wrote:
> Hi,
>That is the problem. Yet i do not know whether it is working fine
> not.i have been working with that for nearly 9-10months but not
> satisfied yet.
> In the following mail i will cut and paste the force field parame
Hi,
That is the problem. Yet i do not know whether it is working fine
not.i have been working with that for nearly 9-10months but not
satisfied yet.
In the following mail i will cut and paste the force field parameters which
you can use it with amber. If you have time please go ahead and mod
Dear Sir,
It will be of great help to send the force field. actually I want to know
whether it was working fine for u or not ?? ... Pls send the file and if
it's working fine then I think you can deposit it in User contributions in
gromacs repository...
On Thu, Jun 23, 2011 at 2:38 PM, Ramachandr
Why you are doing simulation without chromophore? Chromophore is important
in GFP. If you want i can send you the forcefield which i am using for GFP.
Rama
On Wed, Jun 22, 2011 at 10:29 PM, bharat gupta wrote:
> Hi Sir,
>
> Actually I am doing the simulation without the chromophore. So, planarit
Hi Sir,
Actually I am doing the simulation without the chromophore. So, planarity
does not matter to be ..
On Thu, Jun 23, 2011 at 2:23 PM, Ramachandran G wrote:
> Hi Bharat,
> I used Amber force field, but still i am not statisfied with the
> parameters which i used because after some na
Hi Bharat,
I used Amber force field, but still i am not statisfied with the
parameters which i used because after some nanosecond simulation(1 -2 ns)
the planarity of the sturcture changes. I tired changing the force constant
but still not much successfull. If you got success please let me know
Hi,
I want to simulate a docked complex of my protein (GFP) with
phosphotyrosine. I have found this - ffG43a1p forcefield contains parameters
for pTYR, so I want to know how good is this FF for simulating my system...
As in the literature its mentioned that people have used CHARMM, AMBER, OPLS
ff
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