AMBER Archive (2009)

Subject: Re: [AMBER] glycam and solvateoct command

From: Heath Watts (hwatts_at_geosc.psu.edu)
Date: Tue Feb 17 2009 - 16:31:35 CST

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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> AMBER_at_ambermd.org
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>
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