[gmx-users] protein fragmented issue for minimization

MD refmac5 at gmail.com
Wed Dec 13 19:27:53 CET 2017


How about letting gromacs think that it is one protein with two chains?

Ming

On Wed, Dec 13, 2017 at 12:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/13/17 12:52 PM, MD wrote:
>
>> Hi Gromacs folks,
>>
>> I was trying to minimize a structure of a fragmented protein (part of a
>> loop is missing) which makes gromacs keep giving me error messages like
>> bad
>> waters, or warnings of nonbonded interactions between particles xxx and
>> xxx.
>>
>> Is there a solution to let gmx acknowledge the broken structure to start
>> with, or I have to manually connect the broken loop in an artificial way?
>>
>
> You have to model the loop in. It doesn't make sense to try to simulate a
> discontinuous protein.
>
> -Justin
>
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