Dear All
I want to generate a topology file in 43A1 force field for a small molecule.
Of course I want one which contains all hydrogens in that.
PRODRG doesn't generate like this.do you know another server with these
conditions?
Thanks in advance
Mohsen
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gmx-users mailing list
Dear gromacs users
I am using hpc system of our university to work on molecular dynamics
simulation with gromacs. The gormacs has been installed there and I can connect
to the hpc system and submit my jobs.
Now I want to know that for using gnuplot to have my graphs, the gnuplot
program should
Hey,
you want to install gnuplot on your local system. As most of the
analysis, plotting is most
likely done on our local machine.
Without knowledge of your system this is just a stab in the dark.
For linux, open a terminal and type
sudo apt-get install gnuplot
or open the software install
Hi Mohsen,
So you want to have a topology with all atoms for use in a united atom force
field? Seems a bit awkward... PRODRG will only include polar hydrogens, in
accordance with the GROMOS force field. It won't be a particular trustworthy
topology, though, but you've probably caught the words of
Dear gmx users,
I am using gromacs (version 4.0.7) first time
to setup a 2-butoxyethanol-water simulation.
I created topology and coordinate file for BE using PRODRG server.
Then a generated a box containing 20 BE and 480 water molecules using
genbox.
Now, when I am
Dear Dr.Tsjerk
I know it.I know PRODRG is not very valid for evaluating free
energies(According to Dr.Justin article) too.
But the problem is here:
If I know all of hydrigenes are polar,how can I have a topology with all of
them?
Actually there are so many polar H in my small molecules which are
Hi Mohsen,
Now I wouldn't want to get in the way of excellent ideas :)
Check the PRODRG FAQ. It is explained there (somewhere) how to force
inclusion of hydrogens.
Cheers,
Tsjerk
On Feb 6, 2011 11:39 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com
wrote:
Dear Dr.Tsjerk
I know it.I know
mohsen ramezanpour wrote:
Dear All
I read charge groups section in the gromacs manual.
I have a question.please let me know it's answer.
Is it necessary that our charge groups be made of afew number of atoms?
in the other words ,if I have a charge group with 50 atom,Is my results
valid?
Rini Gupta wrote:
Dear gmx users,
I am using gromacs (version 4.0.7) first time
to setup a 2-butoxyethanol-water simulation.
I created topology and coordinate file for BE using PRODRG server.
Then a generated a box containing 20 BE and 480 water molecules using
genbox.
Now, when I am trying
htmldiv
Dear All
I searched my problem in users mailing list but I could not find the
answer. please help me with this.
I am learning the CG Martini force
filed using the tutorial
protein in water for protein ubiquitin. so I did the things like
below:
1. awk -f atom2cg_v2.1.awk 1UBQ.pdb
Faezeh Kargar wrote:
Dear All
I searched my problem in users mailing list but I could not find the
answer. please help me with this.
I am learning the CG Martini force filed using the tutorial protein in
water for protein ubiquitin. so I did the things like below:
1. awk -f
Hi.
I have some problems using ff_charmm27 ported in gromacs 4.5.3.
1) I want to build a topology of phosphorylated tyrosine in one
position of activated protein. I can make it with swissparam.ch server
(getting .itp) or by my hands. But the situation is complicated enough
for me, because of
Алексей Раевский wrote:
Hi.
I have some problems using ff_charmm27 ported in gromacs 4.5.3.
The CHARMM ports are no longer necessary; CHARMM27 is incorporated into Gromacs
4.5.3 by default.
1) I want to build a topology of phosphorylated tyrosine in one
position of activated protein. I
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