Dear Sangita Kachhap,
- From our tests, you do not need any frcmod file as the script3.ff is
loaded by the script1.ff
See: http://q4md-forcefieldtools.org/REDDB/projects/F-90/script3.ff
http://q4md-forcefieldtools.org/REDDB/projects/F-90/script1.ff
You can obviously add on the top of Amber99SB and script3.ff your own
set of force field parameters:
# load Amber 99
parm99 = loadamberparams parm99.dat
# load Amber99SB
frcmod99SB = loadamberparams frcmod.ff99SB
# load the script3.ff
FRCMOD = loadamberparams script3.ff
# load your own set of FF parameters
FRCMOD2 = loadamberparams parm-Sangita.cmd
- You do not need to convert a mol2 file into an off file; indeed both
file formats have the same role: to be a force field library file
format.
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
&
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
- If you want to look at ATP by itself, you can directly used the mol2
file and transform it into the prmtop/prmcrd files.
See the command:
########## Activate the 196 lines below: perl -p -i.old -e
's/\#\#\#\#\#\# //g' script1.ff
at the end of the script1.ff file
- If you want to study the interaction of ATP with a macromolecule;
LEaP does not recognize yet a force field library composed of several
residues; you need to transform the mol2 file into a single residue
with residue and atom names that match these in the PDB file
(macromolecule + ATP). Obviously, two atoms cannot share the same name
in a given residue...
regards, 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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Received on Tue Mar 06 2012 - 02:00:02 PST
