[AMBER-Developers] non-neutral ethane from antechamber

From: Crowley, Michael <Michael.Crowley.nrel.gov>
Date: Tue, 31 Jan 2012 11:41:40 -0700

Hi Everyone,
I wonder if there is something wrong with either my approach or with the
antechamber process.
Something as simple as ethane gives charges that do not add to zero
input pdb attached and output mol2 file.
This is the command:

 antechamber -i ethane.pdb -fi pdb -o ethane.mol2 -fo mol2 -c bcc -s 2

We use Amber, Namd, and charmm a lot imoving between programs for
different purposes on the same system and it is pretty important that each
program is getting the forces right for each force field.
In an effort to test force fields in each program (we are also testing
gromacs and LAMMPS, though we donšt use them much), we are making some
simple test cases.
This test is meant to test amber ff (gaff in this case) in the other
programs and compare results to amber.
We create simple molecules in the amber process and then run them in the
other programs converting input as needed.
Problem starts with antechamber, giving a non-neutral alkane.
If I manipulate the charges to be neutral, we can continue, but I think
antechamber should do that.
Am I expecting too much? Is the collective wisdom on antechamber that it
is imprecise enough that manipulating the charges is no worse than what
you are getting anyway?

Thanks for any ideas or help,

Michael F. Crowley, Ph.D.
Principal Scientist, Biomolecular Sciences Division
National Renewable Energy Laboratory
1617 Cole Blvd.
Golden, CO 80401
303-384-6345 office
303-887-0149 cell
On 1/31/12 10:44 AM, "George Tzotzos" <gtzotzos.me.com> wrote:
>Hi Dwight
>Following your very useful suggestions, I have two additional queries.
>1. Since you selected specific atoms in your receptor mask, what
>criterion did you use to define the initial distance (r2) between the
>ligand and the receptor?
>2. What criterion did you use to define rk2  which I assume is in
>kcal/mol-A^2 . Isn't the value (=500.0) on the high side?
>With thanks
>On Jan 25, 2012, at 3:06 AM, Dwight McGee wrote:
>> Hi George,
>> If you are trying to identify pathways, then it is better to use a
>> of mass restraint like you stated. I have attached an example of how I
>> specified it for my system. The flag "igr1" is the mask for the atoms in
>> the receptor, where I only chose "CA" atoms for the mask. I am not sure
>> what protein you are performing steered molecular dynamics on, but if
>> are such things as flaps that lie over the active site, then you will
>> want to include those in the "igr1" mask.  The flag "igr2" signifies
>> belonging to the ligand in which I only included the heavy atoms; the
>> hydrogens were not included.
>> On Tue, Jan 24, 2012 at 8:40 AM, George Tzotzos <gtzotzos.me.com> wrote:
>>> Hi everybody,
>>> I'm a complete novice in this and I'm trying to follow the Manual.
>>> In summary, I'm trying to identify receptor tunnel(s) through which a
>>> ligand can be released from the binding pocket.
>>> I'm using the restraint and input files attached at the end of this
>>> message.
>>> As can be seen from the .rst file, I'm changing the restraint between
>>> atoms. I have a feeling that this is wrong. Wouldn't it be better to
>>> something like a distant restraint between the centre of mass of the
>>> protein and the ligand? If so, how can one define these centres? In
>>> case, I assume that the iat variable would have to be changed. To what?
>>> A second question relates to the directionality of the "push"? Is there
>>> one? Should one repeat the simulation using different atoms within the
>>> binding pocket of the protein?
>>> Apologies if these questions are naive but I need to start from
>>> and I'm not at all familiar with restraints applied in NMR.
>>> Thanks in advance for any help
>>> George
>>> ======================
>>> dist.RST
>>> # Change distance restraint between atoms
>>> &rst iat=1533,2223, r2=4.492, rk2=14.0, r2a=18.0 /
>>>             #1533 (protein atom); 2223 (ligand atom)
>>> smd.in
>>> smd 2wc6-bombykol
>>> &cntrl
>>> imin=0,irest=1,ntx=5,
>>> nstlim=1000,dt=0.002,
>>> ntc=2,ntf=2,
>>> cut=8.0, ntb=2, ntp=1, taup=2.0,
>>> ntpr=1, ntwx=1, ntwr=1,
>>> ntt=3, gamma_ln=2.0, ig=-1,
>>> temp0=300.0,
>>> jar=1,
>>> /
>>> &wt TYPE='DUMPFREQ', istep1=1, /
>>> &wt TYPE='END', /
>>> DISANG=dist.RST
>>> DUMPAVE=dist_vs_t
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> -- 
>> T. Dwight McGee Jr.
>> Quantum Theory Project
>> University of Florida
>> Graduate Student
>> dwight.mcgee.gmail.com
>> "Problems cannot be solved at the same level of awareness that created
>> them."
>>                Albert Einstein
>> <dist.RST.nfv.mut.orig>_______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Jan 31 2012 - 11:00:03 PST
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