AMBER Archive (2005)

Subject: AMBER: problem with input files when using ff02EP + pol3

From: Phineus Markwick (markwick_at_embl-heidelberg.de)
Date: Sun Apr 03 2005 - 07:35:28 CDT

Dear AMBERers,

I am trying to compare results from MD simulations using polarisable and
non-polarisable force-fields (ie. ff99 + TIP3P vs.
 ff02EP + pol3). I have problems with the input files for the
polarisable force-fields:

I have applied bugfix19 for AMBER7 concerning the ff02EP force-field.
Using my protonated pdb file (xrayH.pdb), I first use the following
tleap script:

source leaprc.ff99
prot = loadpdb xrayH.pdb
solvatebox prot WATBOX 216 10
addions2 prot Na+ 0
check prot
saveamberparm prot prot.parm7 prot.crd
quit

On the 'check' command I get no warnings.

I then use ambpdb to get a pdb file of the solvated system:

ambpdb -p prot.parm7 < prot.crd > prot.pdb

I now use a second tleap script:

source leaprc.ff02EP
loadamberparams frcmod.pol3
WAT = PL3
POLprot = loadpdb prot.pdb
check POLprot
saveamberparmpol POLprot POLprot.parm7 POLprot.crd
quit

On loading the pdb file I am told that numerous 'atoms' are missing...
these turn out to be the
1EP+ and 1EP- point charges that mimic the presence of the electron lone
pairs. On the check
command I get a large number of warnings of close contacts between the
point charges.

On using ambpdb again, I can see the point charges as 'atoms' in my pdb
file:
......
ATOM 20 C MET 1 16.683 16.050 14.857
ATOM 21 O MET 1 17.094 16.620 13.839
ATOM 22 1EP+ MET 1 17.230 16.433 13.576
ATOM 23 1EP- MET 1 17.074 16.969 13.814
ATOM 24 N THR 2 16.180 16.671 15.891
ATOM 25 H THR 2 15.817 16.140 16.669
.......

I then try to perform a short minimsation of the solvent keeping the
solute fixed at contant volume.
The input script (min.inp) is:

&cntrl
imin=1, maxcyc=200,
ntpr=5, ipol=1,
ntr=1,
&end
Group restrained atoms
100.0
RES 1 65
END
END

When I set off this short minimisation routine, I get the error message:

 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info not found in inpcrd

The same minimisation script ran through with no problems when I used
the ff99+TIP3P
force-fields for the same system. Have I done something wrong?

I came across the idea that maybe in the AMBER7 version, PME was not
implemented with polarisable force-fields,
and tried the same minimsation as above, but using the use_pme=0
command, this results in the error message, that
'use_pme' is a variable that is not in Namelist.

I would be grateful if anybody could inform me as to what I have done wrong.

many thanks in advance,
Phineus.

 

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