Re: [AMBER] GAFF atom type for CO

From: Krisztina Feher <feher_krisztina.yahoo.com>
Date: Fri, 21 Jun 2013 02:51:56 -0700 (PDT)

Dear Francois,

the fragment that I have sent contains only the residue for which I would like to get the GAFF atom types and the charges, but of course I ran Antechamber on a tripeptide, thus capping the open valences. The fragment is part of a glycopeptide containing unusual amino acids and linkers, so want to try to model it in GAFF as well as in the macromolecular AMBER forcefield (02). Thank you for the links, I think it will take time to go through them.

best,
Krisztina



--------------------------------------------
On Fri, 6/21/13, FyD <fyd.q4md-forcefieldtools.org> wrote:

 Subject: Re: [AMBER] GAFF atom type for CO
 To: "AMBER Mailing List" <amber.ambermd.org>
 Date: Friday, June 21, 2013, 8:49 AM
 
 Dear Krisztina,
 
 Do you want to perform atom typing for a molecular
 fragment?
 For sure Antechamber will generate errors for the atoms with
 an open 
 valency...
 R.E.D. Python performs atom typing for whole molecules as
 well as 
 their molecular fragments. I will send you a link for
 demonstration; 
 (frcmod & leaprc files are also generated).
 
 So now, I think your best bet is to build a _dipeptide_ i.e.
 cap this 
 fragment with the ACE & NME chemical groups. Then,
 derive the charges 
 and build the force field library(ies) for the central
 fragment (and 
 may be the N-term & C-term fragments):
 See http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
   & may be
     http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#16
     http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#17
 
 You could do that in global approach with R.E.D. Server:
 http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
   and even all automatically from your dipeptide:
 http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#27
 
 Here a limitation in R.E.D. Server is that a computation
 is 
 re-executed if a new input is generated; thus, in the global
 approach 
 a given input is generated several times; with R.E.D. Python
 this will 
 be far more efficient as the inputs are compared before
 execution, and 
 not re-ran if found identical.
 
 Once you got the force field libraries generated by R.E.D.
 and/or 
 R.E.D. Server (mol2 file format: 
 http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php)
 (or mol3 with 
 R.E.D. Python http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php 
 
 with the connecting atoms defined) you can manually define
 the atom 
 types (using a script; See for instance the 'F-93' R.E.DD.B.
 project 
 and its LEaP script:
 http://q4md-forcefieldtools.org/REDDB/projects/F-93/).
 
 Last point: do you plan to incorporate this fragment in a
 protein 
 (from what I understand from the PDB file you sent)? this
 means you 
 need to use a FF for proteins (FF99SB? FF03?) and not
 GAFF...
 
 regards, Francois
 
 
> I would like to assign GAFF atom types to
 diamino-pimelic acid (DAP) 
>  with Antechamber (see attahced pdb file), but the
 carbonyl carbons   
> both on the backbone and on the sidechain as assigned
 &quot;c2&quot; 
>  atom types instead of &quot;c&quot;. I
 embedded DAP in a tripeptide 
>  to derive the atom types and tried both sqm from
 version 12 and   
> divcon from version 9, with sqm being worse
 (assigned   
> &quot;c1&quot;). I tried &quot;-j
 5&quot; option and used -nc 1 for   
> the charge. Is there any way to force an atom type or
 what is it   
> dependent on?
 
 
 
 
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Received on Fri Jun 21 2013 - 03:00:02 PDT
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