Thank you, Justin..
I added the all the needed connectivity for GFP chromophore in the
aminoacid.rtp(mentioned -C and +N to indicate the preceding and
following residue) and also defined the residue as Protein in
residuetypes.dat. For the non existing bond types, bond angles, proper
and improper
Ramachandran G wrote:
Thank you, Justin..
I added the all the needed connectivity for GFP chromophore in the
aminoacid.rtp(mentioned -C and +N to indicate the preceding and
following residue) and also defined the residue as Protein in
residuetypes.dat. For the non existing bond types, bond
Can you perform a simulation of the chromophore alone?
Does that stay stable?
Gerrit
Date: Sat, 13 Nov 2010 12:32:04 -0800
From: Ramachandran G gtr...@gmail.com
Subject: Re: [gmx-users] GFP chromophore topology help
To: jalem...@vt.edu, Discussion list for GROMACS users
gmx-users
Gerrit Groenhof wrote:
Can you perform a simulation of the chromophore alone?
Does that stay stable?
In that regard, some of the information on the following page may be useful:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
-Justin
--
Thank you,
Yes, i did energy minimization to the chromophore alone and it stays
stable
The problem arise when i do the energy minimization to the
GFP-chromophore full system.
It clearly shows the atoms which is expected to connect the
negihbouring residues is flying apart.
I am still
Thank you for the help.
I have successfully constructed the chromphore molecule but
still have problem in connecting it to the neigbhouring residues. I
don't know how the connection sequence needs to be given in gromacs.
Please help
with regards,
Rama
On Tue, Nov 9, 2010 at 3:22 PM,
Thank you for the help.
I have successfully constructed the chromphore molecule but
still have problem in connecting it to the neigbhouring residues. I
don't know how the connection sequence needs to be given in gromacs.
Please help
with regards,
Rama
On Tue, Nov 9, 2010 at 3:22 PM, Justin
Ramachandran G wrote:
Thank you for the help.
I have successfully constructed the chromphore molecule but
still have problem in connecting it to the neigbhouring residues. I
don't know how the connection sequence needs to be given in gromacs.
Please help
You stand a much better
Dear gromacs users:
I have constructed the Amber03 force fields parameters
(bonds,angles, proper and imporer dihedral.) for the chromophore
(p-hydroxybenzylidene-imidazolinone) inside GFP system and got the
topology. But after energy minimization of the system, the
conformation of the
Ramachandran G wrote:
Dear gromacs users:
I have constructed the Amber03 force fields parameters
(bonds,angles, proper and imporer dihedral.) for the chromophore
(p-hydroxybenzylidene-imidazolinone) inside GFP system and got the
topology. But after energy minimization of the
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