I hope you understand that I canNOT fix the problem by just looking
at several thousands on numbers in your topology... My preliminary
guess would be that the problem is localized in the dihedral section,
i.e. you don't define all the necessary dihedrals or define some of
them inconsistently with
Vasilii,
Telling the truth, I don't already remember what was wrong with CNT
topology generation from the coordinate file but I didn't succeed with
any version starting from 3.3.3. So I still keep x2top (3.3.1) for the
CNTs.
There was also several reports in gmx-list that x2top(4.0.X) behaves str
Hmm... I've been using the 4.0.4 x2top to create OPLS-AA topologies for,
e.g., graphane, and it worked more or less right "out of the box", giving
very convincing results. What's the problem exactly about recent versions of
x2top? I use the -noparams option to leave everything having to do with
num
Giulio,
I suggest you to try x2top which is spread with gromacs-3.3.1. The
newer versions of x2top are not sain.
Vitaly
On Thu, Jul 30, 2009 at 1:48 PM, Giulio Scocchi wrote:
> Hi Vitaly
>
> Well, I have downloaded it just a couple of months ago, so I guess it should
> be 4.0.4
>
> Giulio
>
> -
Hi,
What's the version of your gromacs?
~ Vitaly
>
> I am a Gromacs beginner and I am trying to simulate an infinite graphene
> lattice (see 07.29.09 posts - I don't know how to reply directly to
> posts, can someone tell me how to do that?). Mark suggested having a
> look at http://www.gromacs
Hello, when I follow http://cs86.com/CNSE/SWNT.htm and ran:
x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp
I got the following message:
Can not find forcefield for atom C-143 with 2 bonds
Can not find forcefield for atom C-144 with 2 bonds
-
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