Re: [AMBER] nativecontacts command in CPPTRAJ

From: Sowmya Indrakumar <soemya.kemi.dtu.dk>
Date: Sun, 6 May 2018 16:26:52 +0000

Hey Ruth,

Yes, you can include the reference as anything you mention, sorry I forgot to mention it in my previous email. if you don't want to re-image your coordinates, you can avoid this.

Just add the reference flag in the contact command after having defined what the reference structure is.

Also refer to page 600 (http://ambermd.org/doc12/Amber16.pdf) for more info. about the same.

I hope this helps,

Regards

Sowmya

________________________________
From: Ruth Helena Tichauer <rhtichau.laas.fr>
Sent: Sunday, May 6, 2018 5:58:09 PM
To: AMBER Mailing List
Subject: Re: [AMBER] nativecontacts command in CPPTRAJ

Dear Sowmya,

Thank you for your suggestion.

However, I didnít ďwrapĒ the coordinates so, if I understand correct, I donít need to do autoimage, right? Also, I wish to take as a reference the structure I load as a reference rather than the first frame.. Could modifications include these features?

Thank you,

Ruth


> On 6 May 2018, at 17:13, Sowmya Indrakumar <soemya.kemi.dtu.dk> wrote:
>
> Hey Ruth,
>
> You may want to try this, this works fine for me:
>
>
> parm file.parm7
>
> trajin pH.nc
>
> autoimage
> strip :WAT #optional
> reference min.rst7
> nativecontacts :179&!.CA,C,O,N,H writecontacts nativecontacts.dat resout res noimage distance 8.0 out contacts.out first resoffset 4 contactpdb contacts.pdb byresidue map mapout gnu series seriesout nativeseries.dat
>
> Regards
> Sowmya
>
>
> ________________________________
> From: Ruth Helena Tichauer <rhtichau.laas.fr>
> Sent: Sunday, May 6, 2018 12:31:06 PM
> To: AMBER Mailing List
> Subject: [AMBER] nativecontacts command in CPPTRAJ
>
> Dear Amber users and developers,
>
> Iíve run QM/MM simulations of a protein with its ligand.
>
> While visualising the obtained trajectories, Iíve noticed that a given residue (179) engages in different interactions in the initial structure and during the production phase. To depict this structural rearrangements, I wanted to use the nativecontacts command from CPPTRAJ in a manner that it would calculate the by residue native contacts present in the initial structure, given as a reference, and then show that these native contacts are lost and others are formed (non native contacts become native contacts) using the following input file:
>
> #Load topology and trajectories
> parm ../native2.parm
> trajin ../nat2-0_0_19.nc
> reference ../../../2/Neutralized/nat2_md-qm_0.pdb parm ../native2.parm
>
> #Native contacts analysis
> nativecontacts :179&!.CA,C,O,N,H \
> byresidue resoffset 4 out nat2-0_NC-179.nb \
> noimage distance 8.0 reference \
> writecontacts nat2-0_NC-179.out \
> resout nat2-0_NC-179.resout \
> series seriesout nat2-0_NC-179.nc_vs_t \
> map mapout nat2-0_NC-179 \
>
> Nevertheless I get empty files.. As it is the first time Iím using this command, I suspect there are some errors in it, please help me correct it in order to get the information I wish (native contacts vs time, non native contacts vs time, strength of contacts made, lasting native contacts..).
>
> Thank you in advance,
>
> Ruth
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> AMBER.ambermd.org
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>


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Received on Sun May 06 2018 - 09:30:02 PDT
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