AMBER Archive (2008)

Subject: Re: Re: AMBER: Read trajectories generated by CHARMM

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Mon Apr 28 2008 - 19:58:36 CDT


Hi David,

    Thanks very much for your prompt response.
    The reason is that we can't provide so large a memory required by NMA in CHARMM version we used.

Have a nice day.

---------
Jeffrey

>On Mon, Apr 28, 2008, Jeffrey wrote:
>>
>> I noticed that by setting ismem=1 in AMBER, the memory requirement can
>> be reduced to 1/3, which can be fulfilled by our machines.
>> So I want to know whether AMBER can read the trajectories generated by CHARMM?
>Normal mode caculations use the ismem parameter, which require you to minimize
>a structure first. You could use ptraj to read a CHARMM trajectory, convert
>it to Amber restart format, and give those snapshots to nmode.
>
>> If so, which forcefield should I use?
    
>It would be better to download AmberTools and use NAB (with a GB forcefield)
>to carry out the normal mode analysis. Of course, mixing a CHARMM-generated
>trajectory (with its forcefields) and an Amber analysis (with different force
>fields) is likely to create data that is difficutl to interpret. Is there a
>reason why you don't want to do the normal mode analysis in CHARMM?
>
>...dac
>
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