AMBER Archive (2008)

Subject: Re: AMBER: distance restraint in minimization

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Wed Dec 17 2008 - 14:16:18 CST

I am really sorry about all the e-mails, I found out the problem and it
is in
&wt type='REST’, istep1=0,istep2=5000,value1=0.1,value2=4.0, /
REST should be between ' and ' not ’ and ’

i am terribly sorry about this silly mistake, the minimization is
running now

Taufik Al-Sarraj wrote:
> Hi David,
> Actually that is what i did
> i created a fixbond file that had
> 11 ASN ND2 142 DT O4 2.5
> 11 ASN ND2 143 DT O4 5.5
> 69 ASN ND2 121 DT O4 2.5
> 69 ASN ND2 122 DT O4 5.5
>
> and then i used makeDIST_RST -upb fixbond -pdb CEBP8.pdb -rst RST.f
> and then i added DISANG = RST.f to my *.in file as follows
>
> &cntrl
> imin = 1,
> maxcyc = 20000,
> ncyc = 10000,
> ntb = 1,
> ntr = 0,
> cut = 10,
> nmropt = 1,
> /
> &wt type='REST’, istep1=0,istep2=5000,value1=0.1,value2=4.0, /
> &wt type=’REST’, istep1=5001,istep2=20000,value1=4.0,value2=4.0, /
>
> &wt type=’END’ /
> DISANG = RST2.f
>
> but this gives me an error when i try to run it
> >sander -O -i minimize.in -o CEBP8.out -c CEBP8.inpcrd -p CEBP8.prmtop
> -r CEBP8.rst
>
> At line 841 of file _nmrcal.f
> Fortran runtime error: End of file
>
> I am lost as to whether the problem is my RST file or my input file or
> somewhere else
>
> Thank you Dave,
> Taufik
>
> David A. Case wrote:
>> On Wed, Dec 17, 2008, luzhenw1_at_msu.edu wrote:
>>
>>
>>> For the first one, ' ERROR no map function for O4 T :data= 11 ASN
>>> ND2 142 T O4 2.5'. it seems to me that the name is not defined in
>>> the map. My
>>> way to fix it is just modify the map (map.DG-AMBER ) and use
>>> makeDIST_RST -map option to load the modified map. it works for me
>>> at least.
>>>
>>
>> Usually, if you just have a few restraints, it is easier to create your
>> own RST file by hand than to go through makeDIST_RST. That way, you
>> don't have to worry about maps, and so on.
>>
>> ...dac
>>
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