AMBER Archive (2008)

Subject: Re: AMBER: RMSD of two different molecules

From: JunJun Liu (ljjlp03_at_gmail.com)
Date: Wed Mar 26 2008 - 16:54:11 CDT

Hi dawei,

Thanks for response! I want to know how similar two different molecules
are. Maybe part of the different molecules can be taken out for RMSD
calculation. Or maybe there's a software can calculate similarity of
different molecules?

Thanks!

Junjun

On Wed, 26 Mar 2008 16:39:19 -0400, Da-Wei Li <lidawei_at_gmail.com> wrote:

> hello,
>
> What is the point to do so?
>
> You can only compare molecules with same number of atoms.
>
> dawei
>
> On Wed, Mar 26, 2008 at 3:35 PM, JunJun Liu <ljjlp03_at_gmail.com> wrote:
>> Hello everyone,
>>
>> I have two small molecules with different atom numbers. Is there a way
>> to
>> know the RMSD value between these two different molecules? Can ptraj do
>> this?
>>
>> Thanks in advance!
>>
>> Junjun
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