AMBER Archive (2009)

Subject: Re: [AMBER] antechamber

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Jul 01 2009 - 07:26:39 CDT

Dear Kevin and RAK,

Besides the program limit, what are the criteria for selecting the
conformation of such a big molecule ?

regards, Francois

> The version of Mopac6 that comes with antechamber is dimensioned
> for 100 heavy
> (non hydrogen) atoms and 100 hydrogen atoms. The code is Fortran and
> there is no
> dynamic memory allocation so this is a hard limit. If you want to run larger
> systems you would need to change the parameters in the SIZES file
> and recompile.
>
> Kevin
>
> Quoting Alan <alanwilter_at_gmail.com>:
>
>> 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_at_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

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber