Ok!
in tleap, I use the following commands:
source leaprc.GLYCAM_06
LoadOff ions08.lib
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
As regards the input files, I use the ones of the implicit solvent
calculations (the issues are the same).
Thank you for your help!
Minimization:
&cntrl
imin = 1,
maxcyc = 5000,
ncyc = 2500,
ntb = 0,
igb = 1,
cut = 12.0
/
========================================
Heating
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 0,
cut = 12.0,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 10000,
dt = 0.002,
ntpr = 100,
ntwx = 100,
ntwr = 1000
/
Restrain
10.0
RES 1 19
END
END
===========================================================================
Dynamics
&cntrl
imin = 0,
irest = 1,
ntx = 7,
ntb = 0,
ntc = 2,
ntf = 2,
igb = 1,
ntpr = 100,
ntwx = 100,
ntt = 3,
gamma_ln = 1.0,
tempi = 300.0,
temp0 = 300.0,
nstlim = 100000,
dt = 0.001,
cut = 12.0
/
Def. Quota "Lachele Foley (Lists)" <lf.list.gmail.com>:
> This probably isn't the force field, but rather how you are setting up
> or running your simulation.
>
> Can you send me (or post) the commands you used in leap to build the
> structures? Also, please include the mdin (control input) files.
>
>
> On Fri, Feb 17, 2012 at 6:35 AM, <tommaso.casalini.mail.polimi.it> wrote:
>> 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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>
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