Re: [AMBER] ATP minimization

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Tue, 6 Mar 2012 11:28:33 +0530 (IST)

Hello Francois

I have generated .off file for ATP using P2M, P1, P1, BN but when I am genating
frcmod file some of the parameter are missing.Since P2M, P1, P1, BN combination
was not there in script1.ff I have added this combination in this file and
geneated ATP3.mol2.earlier I generated .off file according to combination given
in script1.ff i.e. P2M, P1, P1, B5 but when I matched atom of ATP generated by
this combination with atom of ATP present in pdb of my protein having ATP, were
not matching there is no O5' which I have generated so I have added combination
P2M, P1, P1, BN.

So what I should do next to generate all the missing parameter in .frcmod file.

Here I am attaching .pdb file of ATP present in preotein .pdb file, .mol2,
.frcmod and .off file, I have genareted.

So please suggest me how to solve this problem.



> Dear Sangita Kachhap,
>
> get F-90.tar.bz2
>
> tar jxvf F-90.tar.bz2
> cd F-90
> perl -p -i.old -e 's/\#\#\!\# //g' script1.ff
> grep -v "to be replaced by the correct tripos" script1.ff > script1-new.ff
> tleap -f script1-new.ff
>
> regards, Francois
>
>
> See also in case you want to generate the prmtop/prmcrd files:
> perl -p -i.old -e 's/\#\#\#\#\#\# //g' script1.ff
> or may be adapt it:
> perl -p -i.old -e 's/\#\#\#\#\#\# //g' script1-new.ff
>
>
>> I have already done these (subsitution of #)got the same error:
>>
>>> ########## Activate the 89 lines below: perl -p -i.old -e
>>> 's/\#\#\!\# //g'
>> script1.ff
>>> POP = loadmol2 ./tripos1.mol2
>> Could not open file ./tripos1.mol2: No such file or directory
>>
>> I think directory from where I am running working should have
>> tripos.mol2 file
>> fore adenosine, triphosphate.
>>
>> Am I right? If it is so then from where I can get these tripos.mol2 file for
>> adenosine and triphosphate or I am interpreting something wrong.
>> Please help me to get ride of these confusion.
>>
>>
>>
>>
>>> Dear Sangita Kachhap,
>>>
>>>> I have not able run this command
>>>>
>>>> Shall I use link you have given in command line:
>>>> xleap -f
>>>> http://q4md-forcefieldtools.org/REDDB/projects/F-90/script1.ff
>>>
>>> I ask you to excuse me; presenting this command was a bad idea...
>>> This is just a project ;-)
>>>
>>>> or I have to run command:
>>>> xleap -f script1.ff
>>>
>>> Yes this is the command you have to run...
>>>
>>>> I have tried both fist one didnt run
>>>>
>>>> When try second, Its showing
>>>>
>>>>> POP = loadmol2 ./tripos1.mol2
>>>> Could not open file ./tripos1.mol2: No such file or directory
>>>
>>> Read the file script1.ff and you will see the following commands:
>>>
>>> ########## Activate the 89 lines below: perl -p -i.old -e
>>> 's/\#\#\!\# //g' script1.ff
>>> ########## Remove the 89 lines below: grep -v "to be replaced by the
>>> correct tripos" script1.ff > script1-new.ff
>>>
>>> these two commands have to be executed so that the mol2 file names
>>> generated by R.E.D. corresponds to these stored in R.E.DD.B.
>>>
>>> then xleap -f script1-new.ff
>>>
>>> regards, Francois
>
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


With regards

Sangita Kachhap
SRF
BIC,IMTECH
CHANDIGARH
______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
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Received on Mon Mar 05 2012 - 22:00:02 PST
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