AMBER Archive (2008)

Subject: Re: AMBER: peptide MD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Oct 27 2008 - 12:35:57 CDT

have you tried loading your pdb into leap following the tutorials?
should be straightforward unless you didn't have a structure. maybe
I'm not understanding what the problem is...

On Mon, Oct 27, 2008 at 1:13 PM, Beale, John <jbeale_at_stlcop.edu> wrote:
> I have a PDB file, no constraints.
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Carlos Simmerling
> Sent: Monday, October 27, 2008 12:05 PM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: peptide MD
>
> it depends a lot on whether you have a structure or not, or any
> constraints.
>
> On 10/27/08, Beale, John <jbeale_at_stlcop.edu> wrote:
>> I need to set up a system to use MD simulate the interaction of two
>> decameric peptides in explicit solvent. I need some guidance. Can I
> use
>> LEaP to set up such a system? How do I proceed?
>>
>>
>>
>> John
>>
>>
>>
>>
>
>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Professor, Department of Chemistry
> CMM Bldg, Room G80 Phone: (631) 632-1336 Fax: 632-1555
> Stony Brook University E-mail: carlos.simmerling_at_gmail.com
> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> ===================================================================
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu