AMBER Archive (2007)

Subject: AMBER: Polarizable potentials

From: Denis Courtier (amber982_at_gmail.com)
Date: Mon Nov 26 2007 - 12:49:33 CST

Hello.

I am trying to run a NAc-proline molecule in a polarizable potential.

I have my pdb file. So, I used antechamber,
$AMBERHOME/exe/antechamber -i napro.pdb -fi pdb -o napro.prepin -fo
prepi -c bcc -s 2
$AMBERHOME/exe/parmchk -i napro.prepin -f prepi -o pro.frcmod

Now, i want to charge the polarizable potential:

$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff02polEP.r1

into Xleap windown:

source leaprc.ff02pol.r1
loadamberprep napro.prepin
loadamberparams napro.frcmod
solvatebox X POL3BOX 11
saveamberparmpol X napro.prmtop napro.inpcrd

But i get the following message:

Checking Unit.
Building topology.
Building atom parameters.
For atom: .R<UNK 1>.A<C10 1> Could not find type: c3
For atom: .R<UNK 1>.A<H20 2> Could not find type: hc
For atom: .R<UNK 1>.A<H21 3> Could not find type: hc
For atom: .R<UNK 1>.A<H22 4> Could not find type: hc
For atom: .R<UNK 1>.A<C11 5> Could not find type: c
For atom: .R<UNK 1>.A<O12 6> Could not find type: o
For atom: .R<UNK 1>.A<N2 7> Could not find type: n
For atom: .R<UNK 1>.A<C1 8> Could not find type: c3
For atom: .R<UNK 1>.A<H13 9> Could not find type: h1
For atom: .R<UNK 1>.A<H14 10> Could not find type: h1
For atom: .R<UNK 1>.A<C7 11> Could not find type: c3
For atom: .R<UNK 1>.A<H18 12> Could not find type: hc
For atom: .R<UNK 1>.A<H19 13> Could not find type: hc
For atom: .R<UNK 1>.A<C6 14> Could not find type: c3
For atom: .R<UNK 1>.A<H16 15> Could not find type: hc
For atom: .R<UNK 1>.A<H17 16> Could not find type: hc
For atom: .R<UNK 1>.A<C3 17> Could not find type: c3
For atom: .R<UNK 1>.A<H15 18> Could not find type: h1
For atom: .R<UNK 1>.A<C4 19> Could not find type: c
For atom: .R<UNK 1>.A<O8 20> Could not find type: oh
For atom: .R<UNK 1>.A<H9 21> Could not find type: ho
For atom: .R<UNK 1>.A<O5 22> Could not find type: o
Parameter file was not saved

So, i have repeated the process but changing "source
leaprc.ff02pol.r1" by "source leaprc.gaff". Then, i have run my
md_classical simulation. But when i have open my mdcrd file by vmd in
the middle of my calculation, the molecule is absolutely illogical.

Can somebody help me. Am i running polarizable potential in a proper
way? When am i setting up my potential? when i am using
"$AMBERHOME/exe/xleap -s -f
$AMBERHOME/dat/leap/cmd/leaprc.ff02polEP.r1" or with "source
leaprc.ff02pol.r1" commands...

Thank you in advance.

Denis.
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