Yes, you were right, upgrading it to 4.5.4 made sure the atom types/charges in
the DNA termini were recognized correctly. This time the topology got generated
with integer charges.
thanks
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org
Kamesh Narasimhan wrote:
I am using Gromacs 4.0.5 and in my ffamber03.rtp I can see that the charges are
as you mentioned.
"H1amber99_170.3520019"
But in my top file the H1 atom of the type amber99_17 gets replaced by the amber99_25 type
so what should have been
amber99_17
I am using Gromacs 4.0.5 and in my ffamber03.rtp I can see that the charges are
as you mentioned.
"H1amber99_170.3520019"
But in my top file the H1 atom of the type amber99_17 gets replaced by the
amber99_25 type
so what should have been
amber99_17 1DG5 H1 19 0
Kamesh Narasimhan wrote:
Hil,
I am trying to simulate a protein-DNA structure using amber03 and end up having
a non-integer charge in topology generation . From the webpage of ffamber on
NA-simulations, I could see this below instruction
"However, for nucleic acids this also often causes p
Hil,
I am trying to simulate a protein-DNA structure using amber03 and end up having
a non-integer charge in topology generation . From the webpage of ffamber on
NA-simulations, I could see this below instruction
"However, for nucleic acids this also often causes pdb2gmx to replace an H atom
On 29/08/2011 1:38 AM, Sajad Ahrari wrote:
Dear users,
is there any command in Gromacs to show fluctuations of distance,
between mass center for two groups of amino-acids in a protein, over
time?
Check out manual section 7.4 for clues about which tools do what, and
chapter 8 for more detail
Use g_dist tool.
On Sun, Aug 28, 2011 at 8:38 AM, Sajad Ahrari wrote:
> Dear users,
> is there any command in Gromacs to show fluctuations of distance, between
> mass center for two groups of amino-acids in a protein, over time?
> thanks,
> sajad
>
> --
> gmx-users mailing listgmx-users@gro
Dear users,
is there any command in Gromacs to show fluctuations of distance, between mass
center for two groups of amino-acids in a protein, over time?
thanks,
sajad--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive
>I am not sure, but I assume if you set new names, new files will be
>created. The checkpoint input files contains important information about
>your coordinates, velocities, states of random number generators for the
>NH coupling That is the reason, why it is necessary for a
>continuous extens
On Sun, 2011-08-28 at 17:55 +0800, Hsin-Lin Chiang wrote:
> Hi Flo,
>
> Thank you for reply.
> I got it.
> But as you see I also indicate the new names for output files.
> Do I get correct result in this kind of situation?
> Or I need to rerun it with "-noappend"
I am not sure, but I assume if y
Hi Flo,
Thank you for reply.
I got it.
But as you see I also indicate the new names for output files.
Do I get correct result in this kind of situation?
Or I need to rerun it with "-noappend"
Sincerely yours,
Hsin-Lin
>Hi,
>
>check the standard options of mdrun with the help flag -h of version
>4
On Sun, 2011-08-28 at 14:21 +0800, Hsin-Lin Chiang wrote:
> Hi,
>
> Is part number in extending simulation in ver.4.5.4 cancelled?
> Below is my shell script,
>
> #!/bin/bash
> a=/stathome/jiangsl/simulation/gromacs/d1GUJ_AB/4md
> #running GROMACS
> /stathome/jiangsl/soft/gromacs-4.5.4/bin/mdrun
g_lie calculates the deltaG= alpha(p - w) + beta(p - w) equation. But when calculating DGbind from g_lie it will
ask for only one term at a time i.e. -Elj for either p or w and -Cqq for either p or w. My question is when
using only p for -Elj and Vl-s el>p for -Cqq, how the LJ and EL
terms calcul
On 27/08/2011 2:42 AM, Delmotte, Antoine wrote:
Oh, thank you so much! That was indeed the error.
It's amazing how these little things can sometimes drive you mad
I think the real lesson is to learn to edit documents that will contain
nothing but text using an editor that can be relied up
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