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.stlcop.edu> wrote:
> I have a PDB file, no constraints.
>
> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of Carlos Simmerling
> Sent: Monday, October 27, 2008 12:05 PM
> To: amber.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.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.gmail.com
> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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Received on Wed Oct 29 2008 - 05:08:04 PDT
