[gmx-users] OPLS C-terminal Capping of Glu residue a bug?

[Erik Lindahl]

Hi Marco,

Download the updated version of OPLS that I put on the site last week 
(Contributions section, IIRC) and check if the problem persists.

Cheers,

Erik


On Friday, August 22, 2003, at 11:46 AM, Marco Ceruso wrote:

>
>
> Hi Erik-
> it was a GLU not a GLY at the C-term
> marco
>
>
>
> -----Original Message-----
> From: gmx-users-admin at gromacs.org 
> [mailto:gmx-users-admin at gromacs.org]On
> Behalf Of Erik Lindahl
> Sent: Friday, August 22, 2003 2:36 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] OPLS C-terminal Capping of Glu residue a bug?
>
>
> Hi Marco,
>
> Thanks, I think we've already fixed this, but I'll check it.
>
> You can change the charge manually in the file top/ffoplsaa-c.tdb.
>
> Don't change the atomtype, though - GLY is special since it doesn't
> have any real sidechain.
>
> Cheers,
>
> Erik
>
> On Friday, August 22, 2003, at 11:24 AM, Marco Ceruso wrote:
>
>>
>> Hi-
>> I was generating the topology for a protein with a Glu residue at the
>> C-terminus and I got an absurd total charge of -0.13
>> It appears that the charge on the C-alpha atom is the culprit. When
>> inside
>> the protein the Ca of Glu is opls_224B with a charge of 0.14, at the
>> C-terminus pdb2gmx labels the Glu as opls_285 with a charge of -0.09.
>> Looking at other topologies the last residues has an opls_283 for Ca
>> with a
>> charge of 0.04, which seems to be the correct charge.
>> Marc
>>
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