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> 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
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Received on Fri Feb 17 2017 - 07:00:02 PST
