Re: [AMBER] Different prmtop with reordered mol2 file

From: Ali Morshedifard via AMBER <>
Date: Wed, 20 Jul 2022 09:33:09 -0700

Dear David,

Thanks for your response.

Yes, I get exactly the same energies. Upon further searching of the
mailing list, I found Jason's response here:

It seems like the difference comes simply from how amber counts the
excluded interactions. Are we safe to ignore this difference then ?



On 7/20/2022 7:22 AM, David A Case wrote:
> On Tue, Jul 19, 2022, Ali Morshedi via AMBER wrote:
>> I'm using tleap to create prmtop files from original.mol2 and from
>> reordered.mol2 which are the same molecule but with a different atom
>> order.
>> Since the bonding is the same, I expect all the bonding-related
>> variables
>> in the created prmtops to be exactly the same. However the prmtops have
>> different NNB values! I'd appreciate it if you could take a look at the
>> attached files and let me know if you see why this is happening.
> Do you get identical energies with the two different prmtop files?
> ...thx...dac

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Received on Thu Aug 04 2022 - 13:35:09 PDT
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