Hi,
ntr = 1 needs a different setting (see doc).
Try:
energy minimization
&cntrl
imin = 1,
maxcyc = 2000,
ncyc = 250,
cut = 10,
ntb = 1,
ntr = 1, restraintmask = ':1-289', restraint_wt = 100.,
/
Gerald.
On 03/25/2014 02:16 PM, Urszula Uciechowska wrote:
>
> hi,
>
> I changed it to RES but still getting error:
>
> My input file is the following:
>
> energy minimization
> &cntrl
> imin = 1,
> maxcyc = 2000,
> ncyc = 250,
> cut = 10,
> ntb = 1,
> ntr = 1,
> /
> Hold the DNA-protein fixed
> RES 1 289
> END
> END
>
> in out I have:
>
> 5. REFERENCE ATOM COORDINATES
>
>
> ----- READING GROUP 1; TITLE:
> Hold the DNA-protein fixed
>
> rfree: Error decoding variable 1 3 from:
> RES
>
> this indicates that your input contains
>
> incorrect information
>
> field 1 was supposed to
>
> have a (1=character, 2=integer, 3=decimal) value
>
> I am using now AMBER11 and have no how to correct it.
>
> /Urszula
>
>> On Tue, Mar 25, 2014, Urszula Uciechowska wrote:
>>>
>>> My complex contains DNA and protein. I would like to use ibelly to keep
>>> frozen the complex and allowed water to move.
>>
>> I'd advise against that (but then I always do!) Consider using restraints
>> to
>> the initial position (ntr=1) rather than the belly.
>>
>>>
>>> energy minimization for DNA and protein
>>> &cntrl
>>> imin = 1,
>>> maxcyc = 2000,
>>> ncyc = 500,
>>> cut = 12,
>>> ntb = 1,
>>> ibelly = 1,
>>> /
>>> RES WAT
>>> END
>>> END
>>>
>>> LOADING THE BELLY ATOMS AS GROUPS
>>>
>>> ----- READING GROUP 1; TITLE:
>>> RES WAT
>>> Number of atoms in this group = 0
>>
>> Note that your group syntax is wrong, and is selecting zero atoms. See
>> the
>> chapter on group selections in the Manual.
>>
>>> NSTEP ENERGY RMS GMAX NAME
>>> NUMBER
>>> 1 -1.0972E+06 NaN 0.0000E+00 N 1
>>>
>>> BOND = 0.0000 ANGLE = 0.0000 DIHED =
>>> 0.0000
>>> VDWAALS = -624.5497 EEL = -1096564.5563 HBOND =
>>> 0.0000
>>> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
>>> 0.0000
>>
>> It's not clear what caused RMS to be NaN (not a number). You should
>> experiment with the input parameters (running short, say 10-step
>> simulations
>> with ntpr=1) until you can get something to work. The fact that you have
>> no
>> bond, angle, etc. energies is suspicious: I suspect that the code may well
>> have a bug if you set ibelly=1, but choose no atoms to be in the belly.
>>
>> Don't be afraid to experiment and try to see what will work.
>>
>> ....dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
>
> -----------------------------------------
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
____________________________________________________________________________
Prof. Gerald MONARD
SRSMC, Université de Lorraine, CNRS
Boulevard des Aiguillettes B.P. 70239
F-54506 Vandoeuvre-les-Nancy, FRANCE
e-mail : Gerald.Monard.univ-lorraine.fr
tel. : +33 (0)383.684.381
fax : +33 (0)383.684.371
web : http://www.monard.info
____________________________________________________________________________
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 25 2014 - 08:30:04 PDT
