Dear Hai and Amber users,
I do know how to calculate the distance between the center of mass of the graphene surface and the center of the mass of the protein. However, I wanted to calculate the distance with the CLOSEST heavy atom in the protein. The Amber15 manual referred to the nativecontact command under the mindist command. I would like guidance in how to use this command to calculate the minimum distance.
Thanks again, Kristin
________________________________________
From: Hai Nguyen [nhai.qn.gmail.com]
Sent: Tuesday, October 20, 2015 2:09 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Measuring distance between protein and graphene surface
I guess you can use cpptraj:
https://urldefense.proofpoint.com/v2/url?u=http-3A__ambermd.org_tutorials_analysis_tutorial0_&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=Xkk5aGQL3IFUzM7WUXU-zK9eI7OCst60LOv0Kg0svG0&s=dOS9F7lEGj-IJ9S7H9COw_6ez-nmuplZpHwTJynbs7U&e=
You can check amber 15 manual for further info.
Hai
On Tue, Oct 20, 2015 at 2:01 PM, Krantzman, Kristin D <KrantzmanK.cofc.edu>
wrote:
> Greetings,
> I have performed a md simulation of a protein adsorbed to a graphene
> surface with pmemd. I would like to calculate the distance between the
> protein and the graphene surface. Could you please guide me on how to
> proceed? Thank you in advance.
> Best, Kristin D. Krantzman
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=Xkk5aGQL3IFUzM7WUXU-zK9eI7OCst60LOv0Kg0svG0&s=eFqTkketNSNhGnWdLdrQXTsIBT2r7yU3ksfVvVNNTQg&e=
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=Xkk5aGQL3IFUzM7WUXU-zK9eI7OCst60LOv0Kg0svG0&s=eFqTkketNSNhGnWdLdrQXTsIBT2r7yU3ksfVvVNNTQg&e=
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 20 2015 - 11:30:05 PDT
