hi Francois,
At last I created the DMF box with antechamber. I did
DMF with antechamber
1. Mol2 using R.E.S.P
2.Antechamber
/opt/amber9/exe/antechamber -fi mol2 -fo prepi -i tripos1.mol2 -o dmf.prepi -c bcc -j 4 -at gaff
then
/opt/amber9/exe/parmchk -i dmf.prepi -o dmf.frcmod -f prepi
then
I changed the charge to what I have in mol2 from R.E.S.P
3. Load dmf.prepi and dmf.frcmod
4. check dmf..... all fine (source leaprc.gaff)
5. then I created a box with 182 residue in a cube.
6. save the prmtop and inpcrd
Now I want to equilibrate the box (at 298K and 1 atm pressure) to get the correct density. Then I will mix it with MEOH. How to do it. Thanks for your great help.
Thanks
abhishek
--- On Thu, 17/9/09, FyD <fyd.q4md-forcefieldtools.org> wrote:
From: FyD <fyd.q4md-forcefieldtools.org>
Subject: Re: [AMBER] DMF solvent box
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Thursday, 17 September, 2009, 7:00 AM
Abhishek,
> Hi I have created the box at last. But I can't save the parameter as prmtop and inpcrd. For DMF its showing bond C-H1 not found ( the problem is H1 in C=O). I checked ff99..dat and I assigned atom type for DMF according to that in script.ff . plz help ME.\
Yes, you need to find an atom type for this alhehyde proton. Here you have several choices.
1) You use antechamber to generate gaff atom types & the frcmod file (if required), or
2) You use the HA atom type (capital letter) for this alhehyde proton (C-HA bond), and you create FF parameters by analogy to CA-HA.
3) You create a new atom type HX for this alhehyde proton, and you create the missing FF parameters involving HX by analogy to HA.
regards, Francois
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Received on Fri Sep 18 2009 - 22:30:01 PDT
