Re: [AMBER] Parmed.py deletedihedral

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 23 Jul 2013 10:30:17 -0400

On Tue, Jul 23, 2013 at 7:43 AM, Aronica, Pietro <
pietro.aronica07.imperial.ac.uk> wrote:

> I have sent the topology file.
>

OK, I've found the problem. The issue is in the VXI (custom) residue, as
I'm sure you're aware. The problem is that you used the atom names "mh"
and "dh" to denote hydrogen atoms, but you did not tell tleap that those
atoms were supposed to be hydrogens. (Indeed, if you look at the
ATOMIC_NUMBER section, all of those atom types have atomic number 64.)

As a result, tleap put the dihedral you're looking for (.33 -- @32 -- @36
-- .37) into the DIHEDRALS_WITHOUT_HYDROGEN section of the topology file.
 ParmEd, on the other hand, looks at the masses of the atoms, determines
that dh and mh types are actually hydrogens, and proceeds to look for them
in the DIHEDRALS_INC_HYDROGEN section of the prmtop... which it cannot find.

You should go back to your original leap file that you used to generate the
prmtop and add the following command to the beginning of the file:

addAtomTypes {
    { "dh" "H" "sp3" }
    { "mh" "H" "sp3" }
    ...
}

for all of the atom types that you added to VXI (ones that are naturally in
gaff should already be properly loaded inside leaprc.gaff -- you can see an
example of the addAtomTypes syntax in there). This is important, since
sander and pmemd should know which atoms are Hs and which are not -- if you
currently use SHAKE on H-atoms only (ntc == ntf == 2), then sander and
pmemd will _not_ apply SHAKE to these atom types as you would expect (at
least to my knowledge they won't).

Another issue I found looking at your topology file is that it appears that
no LJ parameters were set for several of the atom types

Reading input from STDIN...
> printDetails .%d=,m=,f=

The mask .%d=,m=,f= matches 6 atoms:

   ATOM RES RESNAME NAME TYPE LJ Radius LJ Depth Mass
 Charge GB Radius GB Screen
     32 2 VXI CG2 fc 1.9080 0.1094 12.0100
-0.3192 1.7000 0.7200
     33 2 VXI HG21 mh 1.4870 0.0157 1.0080
 0.0791 1.2000 0.8500
     36 2 VXI CD1 dc 0.0000 0.0000 12.0100
 0.0000 1.7000 0.7200
     37 2 VXI HD11 dh 0.0000 0.0000 1.0080
 0.0000 1.2000 0.8500
     38 2 VXI HD12 dh 0.0000 0.0000 1.0080
 0.0000 1.2000 0.8500
     39 2 VXI HD13 dh 0.0000 0.0000 1.0080
 0.0000 1.2000 0.8500

>

If you notice here, the LJ radius and depth for CD1, HD11, HD12, and HD13
are 0. Unless you are specifically testing something here (or disappearing
some atoms through a prmtop-based FEP scheme, no C atom should have 0 VDW.
 Likewise for H atoms attached to carbons (those attached to oxygens have 0
LJ parameters).

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 23 2013 - 08:00:02 PDT
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