AMBER Archive (2009)

Subject: Re: [AMBER] DMF solvent box

From: Abhishek Banerjee (
Date: Sat Sep 19 2009 - 00:24:08 CDT

hi Francois,
                   At last I created the DMF box with antechamber. I did

DMF with antechamber
1. Mol2 using R.E.S.P
/opt/amber9/exe/antechamber -fi mol2 -fo prepi -i tripos1.mol2 -o dmf.prepi -c bcc -j 4 -at gaff
/opt/amber9/exe/parmchk -i dmf.prepi -o dmf.frcmod -f prepi
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.

--- On Thu, 17/9/09, FyD <> wrote:

From: FyD <>
Subject: Re: [AMBER] DMF solvent box
To: "AMBER Mailing List" <>
Date: Thursday, 17 September, 2009, 7:00 AM


>                   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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