Dear Dian,
> I was following the tutorial to run RED to get the charges for my molecule.
> It takes for ever for the gaussian calculation to finish since it is a huge
> molecule (>250 atoms).
I did NOT tell you to compute your entire molecule by using Gaussian
instead of divcon/mopac/sqm ;-) similar problems should append in your
case even if I prefer to use QM than semi-emp.
> Is there any short cut to do this? I mean in
> principle Antechamber should do it, right?
I do NOT support the Antechamber approach.
> Although it didn't generate a
> mol2 file, but the sqm.out file did have the charge information for each
> atom (Mulliken charges). Maybe I am wrong, but can I manual create a mol2
> based on the charges and other bonded terms from ANTECHAMBER_BOND_TYPE? Or
> can I just run the charge calculation with fragment of the molecule, which
> is the center of the peptide for my case, get the parameters of the rest
> and then combine these two parts?
I think I told you all what you have to do in my former email. I am
sorry of this is not clear. Let's take an example:
Imagine you have the following 5 residue long peptide with one
modified amino-acid, AA*:
1 2 3 4 5
Gly-Asp-AA*-Lys-Gly
All peptide bonds should be 'trans' except if you have a good reason
(proline, ..., ???)
-1) Concerning 1 & 5:
. you need terminal fragments for 1 & 5: N-term. and C-term.
. do 1 & 5 bear a charged group? 'Yes' at pH = 7 (the MD conditions)
. do you need to parameterize 1 & 5? 'No' they are already in the
Amber force field topology database (FFTopDB)
-2) Concerning 2 & 4:
. you need central fragments for 2 & 4
. do 2 & 4 bear a charged group? 'Yes' at pH = 7
. do you need to parameterize 2 & 4? 'No' they are already the Amber FFTopDB
-3) Concerning 3:
. you need a central fragment for 3
. does 3 bear a charged group at pH = 7? well, you have to find out ;-)
. do you need to parameterize 3?
-> check in the literature
-> if unknown: 'Yes' see tutorials at q4md-forcefieldtools.org
http://q4md-forcefieldtools.org/Tutorial/
For instance:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
vs
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
I hope this helps...
regards, Francois
> On Tue, Jan 31, 2012 at 11:17 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> Dear Dian,
>>
>>
>> Maybe I should not call it peptide in the first place. It is a fairly big
>>> molecule (>250 atoms) with some parts resemble amino acids like Glu, Gln,
>>> Ser, Arg etc. That's why I treated it as a big ligand. How would you
>>> parameterize a molecule like this in Amber? Could you kindly take a look
>>> at
>>> my pdb file? Many thanks.
>>>
>>
>> You need to:
>> - load the Amber Force Field Topology Database (FFTopDB) to look at which
>> amino-acid residues are already available (i.e. the .off or .lib files).
>> - check the peptide bonds in your peptide: do you really want cis peptide
>> bonds
>> - check the charged groups of your amino-acids in your peptide: for
>> instance, do you really want a COOH group instead of COO(-); at pH 7 the
>> carboxylate group is present
>> - among the amino-acid residues in your peptide isolate these that are not
>> in the Amber FFTopDB: you will need to generate a new force field library
>> for these modified/unknown residues (check in the literature if your
>> modified/unknown residue is not already known/parameterized; search in the
>> Amber and R.E.DD.B. databases as well).
>>
>> Then to learn how to create the central, N-terminal & C-terminal fragments
>> for a modified/unknown residue, read:
>> http://onlinelibrary.wiley.**com/doi/10.1002/jcc.540161106/**abstract<http://onlinelibrary.wiley.com/doi/10.1002/jcc.540161106/abstract>
>>
>> See also tutorials at q4md-forcefieldtools.org
>> http://q4md-forcefieldtools.**org/Tutorial/Tutorial-1.php#10<http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10>
>> http://q4md-forcefieldtools.**org/Tutorial/Tutorial-3.php#24<http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24>
>> http://q4md-forcefieldtools.**org/Tutorial/Tutorial-3.php#25<http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25>
>>
>> regards, Francois
>>
>>
>>
>> On Tue, Jan 31, 2012 at 1:06 AM, FyD <fyd.q4md-forcefieldtools.org>
>>> wrote:
>>>
>>> Dear Dian Jiao,
>>>>
>>>> You should look at the output of the semi-empirical tool used
>>>> (divcon/mopac/sqm/...): It looks like the job failed... My
>>>> understanding is that a job performed with a semi-empirical method
>>>> should be fast (in particular, if the optimization threshold is loose).
>>>>
>>>> You reported "pep.pdb": does it mean an entire peptide is involved in
>>>> the computation? in general, one wants to generate a new force field
>>>> library only for a modified residue; the regular residues are handled
>>>> by the Amber Force Filed Topology DataBase...
>>>>
>>>> regards, Francois
>>>>
>>>>
>>>> > I was trying to model this peptide with the following command:
>>>> >
>>>> > antechamber -i pep.pdb -fi pdb -o pep.mol2 -fo mol2 -c bcc.
>>>> >
>>>> > After about 24 hours, the job "finished" except that it didn't generate
>>>> > pep.mol2 file. All other output files seem okay, including
>>>> > ANTECHAMBER_BOND_TYPE.AC0, ANTECHAMBER_AM1BCC_PRE.AC, sqm.in and
>>>> sqm.out.
>>>> > So what happened to mol2? Was the file written to somewhere else?
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Received on Fri Feb 03 2012 - 00:30:03 PST
