Re: Equilibration of the membrane-protein system done in CHARMM-GUI

From: James Starlight (jmsstarlight_at_gmail.com)
Date: Thu Nov 14 2013 - 07:32:44 CST

Some question about addition of some changes in the system made by means of
CHARM-GUI.
Initially I've buit system which includes protein-ligand and the solvated
bilayer
For example I'd like to change ligands in that complex. I made topology for
new ligand by means of cgenff and replaced it in the PDB of my complex.
Could some one provide me with the example of the psfgen script which can
be used to regenerate PSF file (the only changing is the ligand) for such
complex system ?

James

2013/11/8 James Starlight <jmsstarlight_at_gmail.com>

> Mu issue have been soled by increasing the equilibration time in the 6.6
> stage up to 10ns and increasing damping coefficient from 1 ps to 2ps..
> Now there are no such diffusion during production run.
>
> James
>
>
> 2013/11/7 Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu>
>
>> It sounds easier and less error-prone to just let it move, then recenter
>> the trajectory prior to visualization/analysis.
>>
>>
>> On 11/06/2013 10:29 AM, Sunhwan Jo wrote:
>>
>>> I don't think different barostat can prevent diffusion. What you need is
>>> cancellation of translational momentum only for your protein along XY
>>> dimension, but I do not know if there is any option for that in NAMD.
>>>
>>> by the way what exactly role of the restrains in the equilibration steps
>>>> (some of them are defined via ColVars as I noticed)?
>>>>
>>>
>>> 3 sets of restraints were used.
>>>
>>> 1. protein backbone/sidechain restraint
>>> 2. planar restraint that holds lipid head/tail groups in plane
>>> 3. dihedral restraints that retain chirality of lipid head group and
>>> double bonds
>>>
>>> These are used and gradually removed during STEP6. For more information,
>>> please read our manuscripts or tutorial.
>>>
>>> Best,
>>> Sunhwan
>>>
>>> On Nov 6, 2013, at 9:02 AM, James Starlight <jmsstarlight_at_gmail.com
>>> <mailto:jmsstarlight_at_gmail.com>> wrote:
>>>
>>> Sunhwan.
>>>>
>>>> the RMSD have gradually increased during x-y diffusion and then
>>>> stabilized when protein have reached position. I suppose that Its more
>>>> appropriate to measure msd => Diffusion coefficent (not RMSD) from such
>>>> trajectory but I cant find this possibility in namd. By the way what
>>>> barostat options could prevent such diffusion ? ( I've tried to increase
>>>> constant for coupling to P_bath but there were no any changing).
>>>>
>>>> by the way what exactly role of the restrains in the equilibration steps
>>>> (some of them are defined via ColVars as I noticed)?
>>>>
>>>> James
>>>>
>>>>
>>>> 2013/11/6 Sunhwan Jo <sunhwan_at_uchicago.edu <mailto:sunhwan_at_uchicago.edu
>>>> >>
>>>>
>>>>
>>>> James,
>>>>
>>>> STEP7 inputs provided by CHARMM-GUI comes with no restraints. Under
>>>> such condition, I believe diffusion along membrane is normal. You
>>>> should be able to recenter the protein from the trajectory if
>>>> needed.
>>>>
>>>> Your comment about increased RMSD is interesting, though. Are you
>>>> calculating RMSD after reorientation?
>>>>
>>>> Best,
>>>> Sunhwan
>>>>
>>>> On Nov 6, 2013, at 12:51 AM, James Starlight <
>>>> jmsstarlight_at_gmail.com
>>>> <mailto:jmsstarlight_at_gmail.com>> wrote:
>>>>
>>>> > Dear all,
>>>> >
>>>> >
>>>> > As I've mentioned I had problems with the simulation of the
>>>> protein-membrane complex made in Charm-gui. Briefly I had no
>>>> problems during all equilibration phases but on the 7.1 ptoduction
>>>> run step l've observed the diffusion of the protein as the whole
>>>> (!!!) in the x-y plane of the membrane (analysis of the RMSD
>>>> provides me hight increase in RMSD (up to 10A) during first 2ns
>>>> when such 2D diffusion have been detected). I'm not sure if this
>>>> simulation was OK because I've never seen such motion in X-Y plane
>>>> (previously making long simulation in Gromacs with Langevins
>>>> dynamics and Parinello's barostat). As I've mentioned such motion
>>>> is observed during 7.1 step ( here any restraints are removed from
>>>> the conf file like
>>>> > # planar restraint
>>>> > colvars on
>>>> > exec sed -e "s/Constant \$fc/Constant 0/g"
>>>> membrane_lipid_restraint.namd.col > restraints/$outputname.col
>>>> > colvarsConfig restraints/$outputname.col
>>>> >
>>>> > # dihedral restraint
>>>> > extraBonds yes
>>>> > exec sed -e "s/\$FC/0/g" restraints/dihe.txt >
>>>> restraints/$outputname.dihe
>>>> > extraBondsFile restraints/$outputname.dihe
>>>> >
>>>> > Does I need more prolonged equilibration in case where I simulate
>>>> protein inserted in the membrane ( in comparison to the pure
>>>> bilayer) or may be some additional restrains should be included in
>>>> the 7.1 production run as well ?
>>>> >
>>>> > James
>>>>
>>>>
>>>>
>>>
>>
>

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