On Sun, May 24, 2009 at 8:42 AM, Mark Abraham wrote:
>
>
> ; -CH2-S- 0.7
>>
>
> This is a comment line.
>
>
What's the meaning of the number 0.7 in this comment line?
Thanks!
Yan
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Yan Chai wrote:
On Sun, May 24, 2009 at 8:42 AM, Mark Abraham wrote:
; -CH2-S- 0.7
This is a comment line.
What's the meaning of the number 0.7 in this comment line?
I don't know. Nobody would be likely to know without knowing the full
context, which nobody has bother
Mark Abraham wrote:
Yan Chai wrote:
On Sun, May 24, 2009 at 8:42 AM, Mark Abraham wrote:
; -CH2-S- 0.7
This is a comment line.
What's the meaning of the number 0.7 in this comment line?
multiply by 4.184
I don't know. Nobody would be likely to know without knowing t
Excuse me, I don't understand. Could you please explain more in details on
this? What do you mean to multiply by 4.184? I have seen many similar
numbers following the examples of bonds in the comment lines in the force
field files, but I never understood them.
Thanks!
Yan
On Sun, May 24, 2009 a
Yan Chai wrote:
Excuse me, I don't understand. Could you please explain more in details
on this? What do you mean to multiply by 4.184? I have seen many similar
numbers following the examples of bonds in the comment lines in the
force field files, but I never understood them.
calories to jou
The reason I asked the question was becuase I was trying to understand them
in order to parameterize some bonds myself.
for example, dihedral angles a lot time are clearly commented, so I know
which bonds could use the parameter.
e.g.
#define gd_4180.000 5.86 1
; N-CHn-CHn-OA
hi,gmx-user
I make a molecule *.itp and force field parameters. When I run editconf and
genbox to build a system,there are always a warning like this.
"Warning: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type."
I do
Jinyao Wang wrote:
> hi,gmx-user
>
> I make a molecule *.itp and force field parameters. When I run editconf and
> genbox to build a system,there are always a warning like this. "Warning:
> masses will be determined based on residue and atom names, this can deviate
> from the real mass of the
Hi all,
I am using g_potential to calculate the charge distribution of my system which
consists of a protein layer covalently bound to some fatty acids. The protein
layer by itself would have an overall negative charge but they system as a
whole is neutral. My question is this: When I specif
Hi Johnny,
If for a dihedral the definition only lists two atoms, these signify
the central atoms with any possible substituents. I think this is
explained in Chapter 5 of the manual.
Cheers,
Tsjerk
On Sun, May 24, 2009 at 5:58 PM, Zhanglin Ni wrote:
> The reason I asked the question was becua
Hi
I am a bit confused.
1LW9.pdb = T4 lysozyme
After this command,
pdb2gmx -f 1LW9.pdb -o 1LW9.gro -p 1LW9.top
=> GG 45a3is choosed.
The Gromacs tells me that it carries +8 charges.
As we know, that the amount of charges which the protein carries is
based on pH values. So, my question is
Lin,
Gromacs isn't choosing a specific condition, but rather it building
the protein using a set of defaults. Try looking at the documentation
for pdb2gmx, which clearly states the defaults that the program uses
for assigning the protonation state of the residues of interest.
Given those
Hi Lin,
Please follow the advice to do more background reading on both
biochemistry and molecular dynamics if you aren't doing so already.
The charge is not related to the pH. pH is related to the
concentration of H+ in the solution, but you don't have H+ (H3O+/OH-)
in your solution. The charge i
Hi Bruce,
I was trying to generate topologies for one ligand using topolbuild. For the
same I used the command "*topolbuild -dir
/home/vivek/topolbuild1_2_1/dat/gromacs/ -ff gmx43a1 -n Bromo-WR99210 -r
RESID*"
and it resulted in an error as follow:
*Fatal error.
Source code file: readmol2.c, li
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