Dear Andy,
Thank you for your answer.
Indeed I wish to obtain both native and non native contacts even if I need two different input files. I probably will add the non-native option. However I wonder how I should modify the current input file I’m providing to cpptraj as for example, the matrices containing both native and non native contacts are empty:
#Residue Residue Contacts_00002[nativemap]
179.000 179.000 0.0000
#Residue Residue Contacts_00002[nonnatmap]
179.000 179.000 0.0000
Thank you for any insight on this matter,
Ruth
> On 6 May 2018, at 14:05, Andreas Tosstorff <andreas.tosstorff.cup.uni-muenchen.de> wrote:
>
> Hey Ruth,
> maybe the non-native option of the command is what you are looking for?
>
> Best,
> Andy
>
>
>
>
>> Am 06.05.2018 um 12:31 schrieb Ruth Helena Tichauer <rhtichau.laas.fr>:
>>
>> Dear Amber users and developers,
>>
>> I’ve run QM/MM simulations of a protein with its ligand.
>>
>> While visualising the obtained trajectories, I’ve 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 I’m 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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Received on Sun May 06 2018 - 08:00:03 PDT
