I apologize, it was my fault. I forgot one command.
For the sake of completeness, I use AmberTools 1.4.
The right sequence is:
source leaprc.GLYCAM_06
LoadOff ions08.lib
LoadAmberParams frcmod.ionsjc_tip3p
HA = sequence {OME 4ZB 3YB 4ZB 3YB 4ZB 3YB 4ZB 3YB 4ZB 3YB 4ZB 0YB}
AddIons HA Na+ 0
SaveAmberParm HA HA.prmtop HA.inpcrd
quit
I know that the ions parameters I load are optimized for tip3p water
use, but the simulations I tried to perform are only a trial in order
to see if all works properly. That is, they have no scientific
relevance.
However, when I will have to set up the final system, I must load also
the ff parameters for proteins, since I have BMP2.
I tried to pass the issue by using parmchk and obtaining the entire
list of parameters. I used this command:
parmchk -i HA.mol2 -f mol2 -o HA.frcmod -a 'Y' -p
/programs/amber10/dat/leap/parm/Glycam_06g.dat
The file all.frcmod contains all ff parameters. I repeated the
sequence construction and I loaded the file HA.frcmod as a separated
ff modification file, but the issue still remains.
Thank you all for your help!
Tommaso Casalini, Ph.D. fellow
CFA lab, Politecnico di Milano
Def. Quota "Lachele Foley (Lists)" <lf.list.gmail.com>:
> PS: the reason I asked is because the leap input you provided didn't work.
>
>
> On Fri, Feb 17, 2012 at 8:18 PM, Karl N. Kirschner
> <kkirsch.scai.fraunhofer.de> wrote:
>> Hi Tommaso,
>>
>> I have encountered a similar problem recently, I don't think it
>> involves the glycam06g force field directly, but something with how
>> xleap (didn't try tleap) interprets the force field when sourcing
>> the protein/dna force field. If you look at the output structure of
>> leap, I think you will see that a few of the hydrogen atoms are
>> incorrectly placed. I corrected this by only loading glycam06
>> parameters and suppressing the the protein force field loading
>> (i.e. xleap -s -f leap.in). This then gave me the correct spatial
>> structure of the carbohydrate. (I have not tried to reproduce this
>> error using gleap or sleap.) However, if this works for you, then I
>> think you will need to include the ions into glycam sourcing (I am
>> pretty sure their parameters are sourced with the protein force
>> field only, but not 100% sure about that).
>>
>> Cheers,
>> Karl
>>
>> ----- Original Message -----
>> From: "tommaso casalini" <tommaso.casalini.mail.polimi.it>
>> To: amber.ambermd.org
>> Sent: Friday, February 17, 2012 8:35:00 PM
>> Subject: [AMBER] Issues with hydrogens using glycam force field in Amber 10
>>
>> Dear Amber developers and users,
>> I have a problem with hydrogens, using GLYCAM_06 force field with Amber 10.
>> Glycam parameters version is Glycam_06g.dat.
>> I built hyaluronic acid dodecamer thanks to tleap, since I have to
>> investigate BMP2/HA interactions.
>> However, performing MD simulations and studying trajectories, I found
>> these problems:
>>
>> 1) C-H bond stretches a lot even if I apply SHAKE;
>> 2) hydrogen atoms of methyl and hydroxyl groups rotate, it seems that
>> dihedral force constant is null or something like that.
>>
>> There are some details:
>>
>> I built hyaluronic acid with tleap, loading GLYCAM_06 parameters.
>> The HA chain is a sequence of 3YB and 4ZP units, saturated with OME groups.
>> I did not load any .frcmod file in order to modify ff parameters.
>> I performed simulations both in implicit and explicit solvent, but I
>> can see these issues in both cases.
>> It is very important for me that hydrogens are described properly,
>> since hydrogen bonding is an important interaction in the system I am
>> investigating.
>>
>> I thank in advance for your help!
>>
>> Tommaso Casalini, Ph.D Fellow
>> CFA lab, Politecnico di Milano
>>
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>>
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>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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