[gmx-users] ATP for
Chandan Choudhury
iitdckc at gmail.com
Mon Feb 8 16:31:21 CET 2010
Thanks Tom.
Some how only the negative charges were being added in spreadsheet. So, I
got charge around -12.
I am simulating 1QHH. It has ATP in it, the structure of the ligand in the
rcsb (http://www.pdb.org/pdb/explore/explore.do?structureId=1QHH) shows ATP
with hydrogen.
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Mon, Feb 8, 2010 at 8:34 PM, Thomas Piggot <t.piggot at bristol.ac.uk>wrote:
> Are you sure you added it up correctly? I get a number very close to -4.
>
> There is no hydrogen on the gamma phosphate as it was parameterised in this
> way. If the environment in which your ATP is located suggests that the gamma
> phosphate should be protonated then you need to use other ATP parameters
> which include this hydrogen (such as those in the GROMOS forcefield).
>
>
> Cheers
>
> Tom
>
> Chandan Choudhury wrote:
>
>> Hi Tom!!
>> Thanks for the information. I went through the paper and added the new O3
>> atom type. One unusual thing I noticed was that the sum of the partial
>> charges on the atoms of AT P at the last column of
>> http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/ATP.prepfile is -12.7145. How come fractional? and the hydrogens of phosphate
>> are missing. How can it be overcome?
>> Chandan
>>
>> --
>> Chandan kumar Choudhury
>> NCL, Pune
>> INDIA
>>
>>
>> On Sat, Feb 6, 2010 at 1:13 AM, TJ Piggot <t.piggot at bristol.ac.uk<mailto:
>> t.piggot at bristol.ac.uk>> wrote:
>>
>> >From the Carlson et al. paper where these ATP parameters were
>> published and
>>
>> through choosing the appropriate amber_X atom types from the .atp
>> (and the corresponding values for these types in the nb and bon .itp
>> files). As I mentioned previously you need to add a new O3 atom type
>> to these files based on the information in the Carlson paper.
>>
>> If you have a look at one of the entries from the ffamberXX.rtp file
>> and work out how this is used by pdb2gmx it should become clear what
>> you need to do to add the ATP to the forcefield.
>>
>> Cheers
>>
>> Tom
>>
>>
>> --On Saturday, February 06, 2010 00:05:10 +0530 Chandan Choudhury
>> <iitdckc at gmail.com <mailto:iitdckc at gmail.com>> wrote:
>>
>>
>> Hi Thomas !
>>
>> Creating a new entry in the .rtp, nb.itp needs charge, radius,
>> epsilon
>> values etc. values. Where to get these values
>>
>>
>> Chandan
>>
>> --
>> Chandan kumar Choudhury
>> NCL, Pune
>> INDIA
>>
>>
>>
>> On Fri, Feb 5, 2010 at 6:54 PM, Thomas Piggot
>> <t.piggot at bristol.ac.uk <mailto:t.piggot at bristol.ac.uk>>
>> wrote:
>>
>> Not sure about amb2gmx.pl <http://amb2gmx.pl> or acpypi but you
>>
>> can do this by hand. Consult
>> the GROMACS manual (Chapter 4) for the equations to convert the
>> parameters into GROMACS format.
>>
>> I would also say that the easiest way would be to create a new
>> entry in
>> the .rtp and then also add the appropriate bonded parameters
>> into the
>> bon.itp file, making sure to include the bonded parameters for
>> the new O3
>> atom type. Do note that you need to also add this new atom type
>> for the
>> O3 oxygen into the .atp file and the non-bonded parameters for
>> the atom
>> type into the nb.itp file.
>>
>> You can also add entries into the .hdb to allow pdb2gmx to add the
>> appropriate hydrogens to your ATP if so desired. If not, your
>> input pdb
>> for pdb2gmx will need to have these hydrogens already included.
>>
>> Cheers
>>
>> Tom
>>
>> Chandan Choudhury wrote:
>>
>>
>> Hello gmx users,
>> I need to use ATP's parameter for amber port in gromacs. The
>> atp.prep and
>> frcmod.phos for ATP can be found at
>> http://www.pharmacy.manchester.ac.uk/bryce/a
>> <http://www.pharmacy.manchester.ac.uk/bryce/amber>
>>
>> _mdrun -s spc_25_eq.tpr -cpi state.cpi -c spc_25_eq.pdb -o
>>
>> spc_25_eq.trr -e spc_25_eq.edr -g spc_25_eq.log -append yes_
>>
>> mber <http://www.pharmacy.manchester.ac.uk/bryce/amber>. How can
>>
>> I use it in
>> ffamber.
>> The program amb2gmx.pl <http://amb2gmx.pl> <http://amb2gmx.pl>
>>
>> needs amber to be installed,
>> which is not present. Same with ACPYPI.
>>
>>
>> Any suggestion will be very helpful.
>>
>> Chandan
>>
>>
>> --
>> Chandan kumar Choudhury
>> NCL, Pune
>> INDIA
>>
>>
>>
>> --
>> Thomas Piggot
>> University of Bristol, UK.
>> --
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>>
>>
>>
>> ----------------------
>> TJ Piggot
>>
>> t.piggot at bristol.ac.uk <mailto:t.piggot at bristol.ac.uk>
>>
>> University of Bristol, UK.
>>
>> -- gmx-users mailing list gmx-users at gromacs.org
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> --
> Thomas Piggot
> University of Bristol, UK.
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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