Re: [AMBER] ATP minimization

From: FyD <>
Date: Tue, 06 Mar 2012 10:17:28 +0100

Dear Sangita Kachhap,

- From our tests, you do not need any frcmod file as the script3.ff is
loaded by the 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

- 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
>>>> 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
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