AMBER Archive (2006)

Subject: Re: AMBER: MM-PBSA problem

From: vanessa wai (wai.vanessa_at_gmail.com)
Date: Tue Dec 05 2006 - 19:33:35 CST

Yes, I did patched with the latest bugfixes from amber website.

thanks,
vanessa

On 12/6/06, Ray Luo <rluo_at_uci.edu> wrote:
>
> Have you applied all bugfixes for Amber8? It might be related to
> bugfix.49.
>
>
>
> Ray
>
>
>
> -----Original Message-----
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *vanessa wai
> *Sent:* Sunday, December 03, 2006 5:52 PM
> *To:* amber_at_scripps.edu
> *Subject:* Re: AMBER: MM-PBSA problem
>
>
>
> Hi,
>
> The calculation that I'm doing only involves residues (nucleotides) that
> are 15 Angstrom away from the ligand to speed up the calculation (no NMODE
> as well) and its input is as follow:
>
> @PB
> PROC 2
> REFE 0
> INDI 1.0
> EXDI 80.0
> SCALE 1.0
> LINIT 1500
> PRBRAD 1.6
> #
> RADIOPT 0
> #
> FOCUS 0
> PERFIL 80.0
> CHARGE
> SIZE
> #
> SURFTEN 0.005
> SURFOFF 0.0
> @MM
> DIELC 1.0
> @GB
> IGB 2
> GBSA 1
> SALTCON 0.00
> EXTDIEL 80.0
> INTDIEL 1.0
> #
> SURFTEN 0.0072
> SURFOFF 0.00
> #
> @MS
> PROBE 0.0
>
> Hope you could shed some lights on this problem and thanks in advance for
> helping.
> Really appreciate it.
>
> Regards,
> Vanessa
>
>
> On 12/2/06, *Ray Luo* <rluo_at_uci.edu> wrote:
>
> We need to know more about your calculation …
>
>
>
> Can you attach your mm_pbsa.in file?
>
>
>
> Can you also show the free energies for receptor, ligand and complex? How
> do they agree between PB and GB?
>
>
>
> Best,
>
> Ray
>
>
>
> -----Original Message-----
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *vanessa wai
> *Sent:* Saturday, December 02, 2006 1:08 AM
> *To:* amber_at_scripps.edu
> *Subject:* Re: AMBER: MM-PBSA problem
>
>
>
> hi. I used Amber 8.
>
>
>
> Any ideas?
>
>
>
> Thanks,
>
> Vanessa
>
>
>
>
>
>
>
>
>
>
>

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