Hi,
It's difficult to mix nmropt = 1 with ntr = 1 the way you do (i.e.,
using the old group specification for the position restraint).
What you can do is to use the more recent restraint_wt and restraintmask
keywords (see the relevant section about ntr in the doc).
Your input would then be:
#################
&cntrl
nstlim=20000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=50000, ntwx=100,
temp0=300.0, ntt=1, tautp=2.0, ioutfm=1, ntxo=2, ig=-1,
ntb=2, ntp=1, ntc=2, ntf=2,
nrespa=1, NTR=1, nmropt=1,
restraint_wt = 30., restraintmask = ':1',
&end
&wt type='END'
&end
LISTOUT=POUT
DISANG=restraint_list.dist
################
Gerald.
On 09/23/2014 09:20 PM, George Green wrote:
> I tried the modification you suggested, but still no joy. Still getting the
> same error. It seems to indicate that there is something wrong with the
> distance restraint file. However, I checked and atom numbers, etc seem all
> correct. What do you think?
>
> On Tue, Sep 23, 2014 at 4:30 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>> On Tue, 2014-09-23 at 14:39 +0100, George Green wrote:
>>> I'm trying to run a simulation that uses a single harmonic restraint
>>> simultaneously with a distance restraint. The pmemd simulation crashes
>> with
>>> the following error:
>>>
>>> ################
>>> 5. REFERENCE ATOM COORDINATES
>>>
>>> default_name
>>>
>>> ----- READING GROUP 1; TITLE:
>>> LISTOUT=POUT
>>>
>>>
>>> rfree: Error decoding variable 1 3 from:
>>> DISANG=restraint_list.dist
>>> #################
>>>
>>>
>>> Using just NTR or nmropt on their own seems to work with no problems, so
>> I
>>> think this is a syntax issue. I don't have much experience with
>> restraints,
>>> so I am having difficulty seeing where things are going wrong here.
>>>
>>> My input files are:
>>> ##########################
>>> &cntrl
>>> nstlim=20000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=50000, ntwx=100,
>>> temp0=300.0, ntt=1, tautp=2.0, ioutfm=1, ntxo=2, ig=-1,
>>>
>>> ntb=2, ntp=1, ntc=2, ntf=2,
>>>
>>> nrespa=1, NTR=1, nmropt=1,
>>> &end
>>> &wt type='END'
>>> &end
>>> LISTOUT=POUT
>>> DISANG=restraint_list.dist
>>> Group input for restrained atoms
>>> 30
>>> RES 1
>>
>> This needs to be a residue range. For example:
>>
>> RES 1 100
>>
>> RES 1 50
>>
>> If you just want residue 1:
>>
>> RES 1 1
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> _______________________________________________
>> 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
>
--
____________________________________________________________________________
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 Sep 23 2014 - 13:30:02 PDT
