I didn't even tried antechamber yet, but using my script to check your
pdb and it failed:
ERROR: Atoms TOO close (< 0.5 Ang.)
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Dist (Ang.) Atoms
0.32863 ['HETATM 131 H20 '] ['HETATM 201 H86 ']
Check your pdb.
I do use Pymol too, but I suggest you to do something like, in pymol terminal:
cmd.sculpt_activate('t80p')
for n in range(100): cmd.sculpt_iterate('t80p')
this helps to relax your structure.
Anyway, even doing that antechamber didn't run here:
Total number of electrons: 716; net charge: 0
Running: /Users/alan/Programmes/amber10/bin/mopac.sh
Error: unable to find mopac charges in mopac.out
Is net charge 0?
And yes, your system is bigger than recommended (although sometimes I
got topol for systems at that size). Maybe you should split it in 2.
Cheers,
Alan
On Wed, Jul 1, 2009 at 10:17, R. A.<rabedi72.mail.com> wrote:
> Dear Users
>
> I used pymol for creating my pdb structure and send it to antechamber for
> creating prepin file.
> Later I chacked out this file for any correction of atom type regarding
> to gaff force field.
> after running parmchk I got the error of ATTN, need revision. Also I
> tried to load prepin in
> xleap but I got the entry of type Dummy, atom H10 and also atom C44 not
> created.
> I checked everything related to this errors from archive and tried to fix
> the things based on
> suggestions and comments but the problem still continues. it seems my
> structure is big for this
> calculation as I found from the remarks?!. Any suggestions or comments
> would be grateful. Thank you so
> much in advance.
>
> Regards
> RAK
>
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--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Received on Mon Jul 06 2009 - 12:26:59 PDT
