Hi,
Sorry for the long delay on this. I've unfortunately only just gotten
to it. After looking at your issue again I realized I overlooked
something very important the first time - the mask ':CL3.CL1,CL2,CL3'
selects multiple molecules. The 'centerX' keywords specify that you
want the RDF calculated with respect to the center of *all* atoms in
the mask. This means that you're taking the RDF with respect to the
center of everything selected by that mask. I think that maybe you
were expecting the center of *each*, is that right? So I think that
cpptraj is working as intended here. Let me know if I've missed
something.
Thanks,
-Dan
On Sun, Dec 25, 2016 at 12:54 PM, JAIME RUBIO MARTINEZ
<jaime.rubio.ub.edu> wrote:
>
> Hello,
> With a new test, It seem like a bug in the cpptraj when using center only for the solvent.
> Without center2 :
> radial Rad_M8_CLCen_NH_CHCl3_NoCen2.txt 0.1 10.0 :2.H :CL3.CL1,CL2,CL3 volume
> results are ok:
> #Distance_(Ang) :2.H_=>_:CL3.CL1,CL2,CL3
> 0.050000 0.000000
> 0.150000 0.000000
> 0.250000 0.000000
> 0.350000 0.000000
> 0.450000 0.000000
> 0.550000 0.000000
> 0.650000 0.000000
> 0.750000 0.000000
> 0.850000 0.000000
> 0.950000 0.000000
> 1.050000 0.000000
> 1.150000 0.000000
> 1.250000 0.000000
> 1.350000 0.000000
> 1.450000 0.000397
> 1.550000 0.000000
> 1.650000 0.000613
> 1.750000 0.000272
> 1.850000 0.000244
> 1.950000 0.001316
> 2.050000 0.006947
> 2.150000 0.032482
> 2.250000 0.117318
> 2.350000 0.250289
> ________________________________________
> De: JAIME RUBIO MARTINEZ
> Enviado: miércoles, 21 de diciembre de 2016 17:20
> Para: AMBER Mailing List
> Asunto: Re: [AMBER] rdf_with_center_in_cpptraj_16
>
> Hello,
> Thanks for your suggestion....
>
>
> Curiously, when the center is in the Ala residue results are ok.
> radial Rad_M8_CH3_H1_CHCl3.txt 0.1 10.0 :2.CB,HB1,HB2,HB3 center1 :CL3.H1 volume
>
>
> But with :
>
> radial Rad_M8_CLCen_NH_CHCl3.txt 0.1 10.0 :2.H :CL3.CL1,CL2,CL3 center2 volume
>
> I have different results ... but the same error .......
>
> source /home/prog/amber16/amber.sh
> /home/prog/amber16/bin/cpptraj ./dialanine.top > Radial_M8_CHCl3.out << EOF
> trajin ../minim_num_8_all.nc 1 last 1
> autoimage
> reference da_chcl3_reference_FIRST.pdb
> rmsd reference out rmsd_ff14sb_wat_M8.dat :1-3.CA,N,C
> radial Rad_M8_CLCen_NH_CHCl3.txt 0.1 10.0 :2.H :CL3.CL1,CL2,CL3 center2 volume
> go
> EOF
>
> #Distance_(Ang) :2.H_=>_:CL3.CL1,CL2,CL3
> 0.050000 0.000000
> 0.150000 0.000000
> 0.250000 0.000000
> 0.350000 0.000000
> 0.450000 0.000000
> 0.550000 0.000000
> 0.650000 0.000000
> 0.750000 0.000000
> 0.850000 0.000000
> 0.950000 0.000000
> 1.050000 0.000000
> 1.150000 0.610907
> 1.250000 0.000000
> 1.350000 1.330146
> 1.450000 1.921791
> 1.550000 15.137103
> 1.650000 45.418719
> 1.750000 124.299935
> 1.850000 297.317718
> 1.950000 561.793906
> 2.050000 847.220257
> 2.150000 1120.499190
> 2.250000 1193.650059
> 2.350000 1074.333347
>
> ________________________________________
> De: Daniel Roe [daniel.r.roe.gmail.com]
> Enviado: miércoles, 21 de diciembre de 2016 15:59
> Para: AMBER Mailing List
> Asunto: Re: [AMBER] rdf_with_center_in_cpptraj_16
>
> Hi,
>
> In general for 'radial' you want your first mask to have the most atoms. So try
>
> radial Rad_M8_NH_CLCen_CHCl3.txt 0.1 10.0 :2.H :CL3.CL1,CL2,CL3
> center2 volume
>
> instead and see if that helps.
>
> -Dan
>
> On Wed, Dec 21, 2016 at 8:01 AM, JAIME RUBIO MARTINEZ
> <jaime.rubio.ub.edu> wrote:
>> Hello,
>>
>> I am trying to calculate RDF with cpptraj ( amber16 ) for Dialanine in chloroform.
>>
>> 1) The results when using this expression seem to be ok:
>>
>> radial Rad_M8_CH3_CLCen_CHCl3.txt 0.1 10.0 :2.CB,HB1,HB2,HB3 center1 :CL3.CL1,CL2,CL3 center2 volume
>>
>> #Distance_(Ang) :2.CB,HB1,HB2,HB3_=>_:CL3.CL1,CL2,CL3
>> 0.050 0.000000
>> 0.150 0.000000
>> 0.250 0.000000
>> 0.350 0.000000
>> 0.450 0.000000
>> 0.550 0.000000
>> 0.650 0.000000
>> 0.750 0.000000
>> 0.850 0.000000
>> 0.950 0.000226
>> 1.050 0.000000
>> 1.150 0.000155
>> 1.250 0.000131
>> 1.350 0.000075
>> 1.450 0.000065
>> 1.550 0.000057
>> 1.650 0.000100
>> 1.750 0.000134
>> 1.850 0.000179
>> 1.950 0.000233
>> 2.050 0.000227
>> 2.150 0.000324
>> 2.250 0.000444
>> 2.350 0.000506
>>
>> However this other expression fails and I don't understant why :
>>
>> radial Rad_M8_NH_CLCen_CHCl3.txt 0.1 10.0 :CL3.CL1,CL2,CL3 center1 :2.H volume
>>
>> #Distance_(Ang) :CL3.CL1,CL2,CL3_=>_:2.H
>> 0.050 0.000000
>> 0.150 0.000000
>> 0.250 0.000000
>> 0.350 0.000000
>> 0.450 0.000000
>> 0.550 0.000000
>> 0.650 0.000000
>> 0.750 0.000000
>> 0.850 0.000000
>> 0.950 0.073139
>> 1.050 0.239525
>> 1.150 1.997049
>> 1.250 8.663635
>> 1.350 28.408471
>> 1.450 86.507489
>> 1.550 212.667108
>> 1.650 434.138973
>> 1.750 763.129547
>> 1.850 1130.629447
>> 1.950 1385.868655
>> 2.050 1439.241063
>> 2.150 1242.488203
>> 2.250 892.349340
>> 2.350 539.441398
>>
>>
>>
>>
>> Aquest correu electrònic i els annexos poden contenir informació confidencial o protegida legalment i està adreçat exclusivament a la persona o entitat destinatària. Si no sou el destinatari final o la persona encarregada de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si heu rebut aquest correu electrònic per error, us preguem que n’informeu al remitent i que elimineu del sistema el missatge i el material annex que pugui contenir. Gràcies per la vostra col·laboració.
>>
>> Este correo electrónico y sus anexos pueden contener información confidencial o legalmente protegida y está exclusivamente dirigido a la persona o entidad destinataria. Si usted no es el destinatario final o la persona encargada de recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, distribuirlo, copiarlo ni a revelar su contenido. Si ha recibido este mensaje electrónico por error, le rogamos que informe al remitente y elimine del sistema el mensaje y el material anexo que pueda contener. Gracias por su colaboración.
>>
>> This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration.
>> _______________________________________________
>> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 06 2017 - 05:30:03 PST
