Thank you very much Gustavo!
That was the problem. The correct flag is “nfe”.
When I try to run the simulation, I get now this strange error message:
-----
Pseudocontact shifts will be read from file: pcs.in
namelist no reports error
Number of Total protons 28
Number of paramagnetic center 1
TENSOR PARAMETERS
PHI= ******* TETA= ******* OMEGA= *******
A1= 15.930 A2= 5.489
VIOLATIONS 0 RESIDUALS 0.00000
Invalid stop to time: ^.^.^.^.^.^.^.^.^.^.^@^@^@^@^@^@^@^@^@^@
-----
Best,
Francisco
--
Francisco Corzana
Departamento de Química
Complejo Científico-Tecnológico
Universidad de La Rioja
Madre de Dios, 51.
26006 Logroño (La Rioja) Spain
e-mail: francisco.corzana.unirioja.es
www.francisco-corzana.com <
http://www.francisco-corzana.com/>
Tel +34941299632
-----Mensaje original-----
De: Gustavo Seabra <gustavo.seabra.gmail.com>
Responder a: AMBER Mailing List <amber.ambermd.org>
Fecha: miércoles, 23 de marzo de 2016, 14:34
Para: AMBER Mailing List <amber.ambermd.org>
Asunto: Re: [AMBER] Problems running MD simulations with pseudocontact shifts as restraints
>
>> Em 23 de mar de 2016, à(s) 05:44, Francisco Corzana López <francisco.corzana.unirioja.es> escreveu:
>>
>> Dear all,
>> I am trying to run MD simulations with sander (AMBER14) with pseudocontact shifts as restraints. I get the following error:
>>
>> nameless reports error reading &pcshf
>>
>> I think the problem is related with “nme” and “nmpmc” flags in “pcs.in" file.
>> I have realized that there is a mistake in amber manual: in the example the variable “nmpCM” is used instead of the correct one "nmpMC”
>> I can get rid of the error message by removing the flag “nme” from pcs.in file. However, in this case, as no paramagnetic centers are defined, new errors messages appear.
>> Any clue??
>> Thank you very much in advance.
>> Francisco
>>
>>
>>
>> This is my input file:
>>
>> […]
>
>> And this is the pcs.in file:
>>
>> &pcshf
>> nprot=1,
>> nme=1,
> ^^^^^^
>
>Apparently, this should be “nfe” instead:
>
>From the pcshift.F90 source file:
>
>namelist /pcshf/ nprot,nfe,obs,wt,iprot,tolpro,mltpro, &
> optphi,opttet,optomg, &
> opta1,opta2,optkon,nmpmc
>
>There’s no “nme” in the namelist.
>
>Gustavo.
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Received on Wed Mar 23 2016 - 10:00:03 PDT
