Re: [AMBER] frequency contact maps

From: Antonio Coluccia <antonio.coluccia.uniroma1.it>
Date: Tue, 21 Feb 2017 15:45:00 +0100

Dear Dan
thank you very much
your help was crucial.
At the and i was able to obtain my surface of frequency interaction.
The working input was:
native contact :mask1 :mask2 distance 6 ref reference.pdb savenonnative nncontactpdb file.pdb


My best
Antonio


Antonio Coluccia Ph.D.
Department of Chemistry and Drugs Technology
Rome 00185
Piazzale Aldo Moro 5
antonio.coluccia.uniroma1.it

> On 17 Feb 2017, at 15:48, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> Sorry, I got a little ahead of myself when I wrote to you before. The
> keyword you want is 'contactpdb' for native contacts. The
> 'nncontactpdb' keyword is for non-native contacts and must be
> specified in conjunction with the 'savenonnative' keyword. For the
> full syntax type 'help nativecontacts' while running cpptraj
> interactively.
>
> On Fri, Feb 17, 2017 at 4:04 AM, Antonio Coluccia
> <antonio.coluccia.uniroma1.it <mailto:antonio.coluccia.uniroma1.it>> wrote:
>> this is my input:
>> native contact :1-675&!.H :676-32150!&@H distance 6 ref ref.pdb nncontactpdb file.pdb
>
> Note that the actual command is 'nativecontacts'. Also your second
> mask looks like it has the order of ! and & switched.
>
> -Dan
>
>>
>> Do you have any idea of what’s going wrong
>> Thanks
>>
>>
>> Antonio
>>
>>
>> Antonio Coluccia Ph.D.
>> Department of Chemistry and Drugs Technology
>> Rome 00185
>> Piazzale Aldo Moro 5
>> antonio.coluccia.uniroma1.it
>>
>>> On 15 Feb 2017, at 16:38, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>
>>> Hi,
>>>
>>> In the GitHub version of cpptraj (https://github.com/Amber-MD/cpptraj)
>>> a new keyword has been added to 'nativecontacts':
>>>
>>> nncontactpdb <file>
>>>
>>> which will print out a PDB of the reference frame used to determine
>>> native contacts with the B-factor column assigned a value related to
>>> relative contact strength, with 100 assigned to the strongest contact.
>>> Maybe this is close to what you want?
>>>
>>> -Dan
>>>
>>> On Wed, Feb 15, 2017 at 9:28 AM, antonio.coluccia.uniroma1.it
>>> <antonio.coluccia.uniroma1.it> wrote:
>>>> Dear all,
>>>> I am in trouble with contact map
>>>> i have done some simulations of my protein embedded into water and a
>>>> organic cosolvents (20%) octaedron boxes.
>>>> At this point i would like to generate a 3D map of frequency
>>>> interaction/contact between the protein and the organic solvent molecules.
>>>> Is it possible by cpptraj? I read something about nativecontact but my
>>>> concerns are about the output, is it possible to have 3d maps by
>>>> nativecontatcs.
>>>>
>>>> Thank you very much,
>>>> any help will be really appreciate.
>>>>
>>>> Antonio
>>>>
>>>> --
>>>> Antonio Coluccia, Ph.D.
>>>> Department of Chemistry and Drugs Tecnology
>>>> La Sapienza University
>>>> Rome 00185
>>>> Piazzale Aldo Moro 5
>>>> antonio.coluccia.uniroma1.it
>>>> mobile: 00393406113351
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
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>>>
>>>
>>>
>>> --
>>> -------------------------
>>> Daniel R. Roe
>>> Laboratory of Computational Biology
>>> National Institutes of Health, NHLBI
>>> 5635 Fishers Ln, Rm T900
>>> Rockville MD, 20852
>>> https://www.lobos.nih.gov/lcb
>>>
>>> _______________________________________________
>>> AMBER mailing list
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb <https://www.lobos.nih.gov/lcb>
>
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Received on Tue Feb 21 2017 - 07:00:03 PST
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