Re: [AMBER] frequency contact maps

From: Antonio Coluccia <antonio.coluccia.uniroma1.it>
Date: Fri, 17 Feb 2017 10:04:42 +0100

Dear Dan,
i have followed your advice about the installation of the new cpptraj version.
I have tried many times but i always obtain the following error:
Error: [nativencontac] Not all arguments handled [ nncontatcpdb ]

this is my input:
native contact :1-675&!.H :676-32150!&@H distance 6 ref ref.pdb nncontactpdb file.pdb

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
>>
>>
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>> 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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Received on Fri Feb 17 2017 - 01:30:02 PST
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