[gmx-users] files missing
David
spoel at xray.bmc.uu.se
Thu Aug 11 09:08:23 CEST 2005
On Thu, 2005-08-11 at 10:18 +0530, Rahul Karyappa wrote:
>
> Dear all,
> I ran x2top command to get .top file from .gro. But it gave me error
> for all the forcefields I used. The error was as follows:
> Fatal error: Library file ffG43a1.n2t not found in current dir nor in
> default directories.
> Also when I used other forcefields it gave me same errors but the file
> names were different i.e. ffG43b1.n2t, ffG43a2.n2t, ffoplsaa.n2t and
> ffgmx2.n2t.
> Please tell me where I can get these files. I have searched for these
> files on my pc (/usr/local/gromacs/share/top) but these are not there.
> Waiting for your kind reply.
>
>
>
>
>
> Rahul Karyappa
> NCL, Pune
> India
>
> *****************************************************************
> This email is virus free by TrendMicro Inter Scan Security Suite.
> *****************************************************************
>
Which gromacs version?
I'm attaching the ffgmx version. Are you sure you don't want to use
pdb2gmx (for proteins)?
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-------------- next part --------------
O O 1 C ; CARBONYL OXYGEN (C=O)
O OM 1 C ; CARBOXYL OXYGEN (CO-)
O OA 2 C H ; HYDROXYL OXYGEN (OH)
O OW 2 H H ; WATER OXYGEN
N N 3 H C C ; PEPTIDE NITROGEN (N OR NH)
N NT 3 H H C ; TERMINAL NITROGEN (NH2)
N NL 4 C H H H ; TERMINAL NITROGEN (NH3)
N NR5 2 C C ; AROMATIC N (5-RING,2 BONDS)
N NR5* 3 C C H ; AROMATIC N (5-RING,3 BONDS)
N NP 3 C C FE ; PORPHYRIN NITROGEN
C C 3 C O * ; BARE CARBON (PEPTIDE,C=O,C-N)
; Note that order is importante here because of wildcards.
C C3 4 H H H * ; ALIPHATIC CH3 GROUP
C C2 4 H H C * ; ALIPHATIC CH2 GROUP
C C1 4 H C * * ; ALIPHATIC CH GROUP
C CB 3 C C C ; BARE CARBON (5-,6-RING)
H H 1 N ; HYDROGEN BONDED TO NITROGEN
H HO 1 O ; HYDROXYL HYDROGEN
H HW 1 OW ; WATER HYDROGEN
H HS 1 S ; HYDROGEN BONDED TO SULFUR
H HC 1 C ; HYDROGEN BONDED TO CARBON
More information about the gromacs.org_gmx-users
mailing list