Re: [AMBER] frequency contact maps

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Tue, 21 Feb 2017 10:16:06 -0500

Great, glad to hear it!

Remember that the 'nncontactpdb' will only show you non-native
contacts. The 'contactpdb' keyword will show you native contacts.

-Dan

On Tue, Feb 21, 2017 at 9:45 AM, Antonio Coluccia
<antonio.coluccia.uniroma1.it> wrote:
> 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
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
>>>>
>>>> --
>>>> -------------------------
>>>> 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
>>>>
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>>>
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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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-- 
-------------------------
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
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Received on Tue Feb 21 2017 - 07:30:03 PST
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