Another point: is it possible to use pdb2gmx to do the job instead of
x2top? I tried and used the GROMOS96 43b1 vacuum force field (since the
doping by potassium is in vacuum), but i got the error"Residue 'CNT' not
found in residue topolgy database'. I went to the 'ffg43b1.rtp' file in
the /share/top folder and defined it as '[CNT]
[atoms]
C C 0 0'
but still get the same error.
Your help is much appreciated,
Thank you in advance,
George
George Abadir wrote:
Hi,
I want to make a simulation of CNT in an environment of potassium
atoms to see how they will be adsorbed on the CNT surface (this is a
way of doping carbon nanotubes). I built a .pdb file with a CNT and
some potassium atoms with random coordinates around the nanotube. When
I run x2top to have my topology file, I get the error:"No forcefield
type for atom K with 0 bond". The problem is that the atoms of
potassium should indeed be not bonded to anything at the beginning of
the simulation. Does anybody have a way to describe such a system and
avoid this error?
Thank you very much in advance,
Regards,
George
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
