AMBER Archive (2009)

Subject: Re: [AMBER] glycam and solvateoct command

From: Lachele Foley (Lists) (lf.list_at_gmail.com)
Date: Wed Feb 18 2009 - 09:00:34 CST

> Does typing these two force fields nullify the effect of the glycam force field?

Mostly, the sets are orthogonal. However, the ff03 parameter set
(among others) defines the atom type CG as being sp2, which is bad for
glycam. If you load the parameter sets in the proper order, which you
probably did, leap should ignore the ff03 CG definition and use
glycam's. Alternately, remove the definition in a personal copy of
the ff03 leaprc. If the top and crd files build at all, it's
probably ok, but if you want to be sure everything is fine, then I
suggest loading the resulting topology and coordinate files into VMD
so you can inspect the bonding in the glycan.

My quick inspection of our (possibly outdated) cmd and parm
directories indicates that ff03 doesn't ever use the CG atom type, but
only defines it, so, I would not expect there to be any issues with
other parts of the system -- others with more knowledge of ff03 please
correct me here if I'm wrong... any ff03 folks have comments?

:-) Lachele

On Tue, Feb 17, 2009 at 5:31 PM, Heath Watts <hwatts_at_geosc.psu.edu> wrote:
> Thank you Florent. It seems to work if I type
> $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99 to get to
> xleap,
>
> then if I enter both of these lines:
> source leaprc.gaff
> source learprc.ff03
>
> everything works well.
>
> Does typing these two force fields nullify the effect of the glycam force
> field? Then I can type:
>
> saveamberparm SUS sustiva.prmtop sustiva.inpcrd
> If I omit any of these force fields, I can't build the prmtop or inpcrd
> files.
> Best regards,
> Heath
>
>
>
> On Tue, Feb 17, 2009 at 3:13 PM, Barbault Florent <
> florent.barbault_at_univ-paris-diderot.fr> wrote:
>
>> Hello,
>>
>> As far as I know, glycam04 contains "only" information for carbohydrates
>> but nothing about the solvent. If you want to solvate your system you should
>> load also ff03 (or ff99) to do the 'solvatoct' command.
>>
>> Hope this will help you.
>> Regards
>> Florent Barbault
>>
>>
>> On Tue, 17 Feb 2009 14:51:13 -0500
>> Heath Watts <hwatts_at_geosc.psu.edu> wrote:
>>
>>> Hi,
>>> I'm trying to use the .glycam04 force field to with a glucose model. I am
>>> unable to get AMBER to generate the prmtop and inpcrd files when I use
>>> Cerius 2 to build the pdb file. So, I had to do the following:
>>>
>>> $AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo
>>> prepi -c bcc -s 2
>>>
>>> $AMBERHOME/exe/parmchk -i sustiva.prepin -f prepi -o sustiva.frcmod
>>>
>>> $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
>>>
>>> source leaprc.gaff
>>>
>>> loadamberprep sustiva.prepin
>>>
>>> loadamberparams sustiva.frcmod
>>>
>>> solvateoct SUS TIP3PBOX 8.0
>>>
>>>
>>> This generated the 8.0 A octahedral volume of H2O around my model, as I
>>> wanted it to do.
>>>
>>> However, if I use (everything else is the same):
>>>
>>>
>>> $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.glycam04
>>>
>>> instead of:
>>>
>>> $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
>>>
>>> I get the following message when I run the solvateoct command:
>>>
>>>
>>> solvateOct: Argument #2 is type String must be of type: [unit]
>>>
>>> usage: solvateOct <solute> <solvent> <buffer> [ansio] [closeness]
>>>
>>>
>>> What could be causing this error that prevents me from solvating my model?
>>>
>>> Thanks,
>>> Heath
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER_at_ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> -------------------------------------------------
>> Dr Florent Barbault
>> Maitre de conferences / Assistant professor
>>
>> NEW ADDRESS !!!
>>
>> Universite Paris Diderot
>> Laboratoire ITODYS
>> 15 rue Jean de Baïf, bâtiment Lavoisier
>> 75013 Paris FRANCE
>> http://www.itodys.univ-paris7.fr/
>> tel : (33) 01-57-27-88-50
>> e-mail : florent.barbault_at_univ-paris-diderot.fr
>> -------------------------------------------------
>>
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>>
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-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA

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