AMBER Archive (2008)

Subject: Re: AMBER: Chloride anion ligands leave the protein during MD

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Nov 16 2008 - 05:17:00 CST

Hi Gustavo:

A did an approximate analysis to answer your question. I.e, I examined
...prmtop/..inpcrd, then ...prmtop/min.rst, and then similarly the
various heating steps, at the last frame. The tool was the zone
command in Chimera, i.e., I carried out a mapping of residues around
each Cl-. I understand that this procedure is severely biased by the
examination of a single snapshot, but perhaps it did not deserve
spending more time than that.

As expected, the minimization gave a practically identical mapping as
from inpcrd, only the distances with respect to Cl- were slightly
longer.

Until heat4.mdcrd (although set to 300K, the final temp - for all
snapshots - was ca 290K) the Cl- anions were still at their binding
site. Again, to be exact, more work would be needed.

During heat5.mdcrd one of the Cl- started moving visibly during the
Chimera movie. At frame 16 (out of 30) it was completely out of the
protein, while the others were still in.

I am sure you are not interested in this description. Your point, of
nrespa (which was set to 2 from prod2.in on), becomes immaterial,
however, in the mess I have created.

Curiously (for me, who, as an organic chemist, wants to see the
molecular structures) I was not careful. I examined the energies,
which were more or less OK. But when I saw rmds vs frame 0 going up
linearly with the number of frames, mdcrd should have been examined.

At this point, as I already posted, I would be grateful to GB experts
to express their opinion if it may be worth while to try, starting
perhaps from heat4.rst, by restraining the various Cl- at, say, three
surrounding atoms. I am very uncertain if that may be a sound move. I
fear to give erroneous bias to the system.

Thanks

francesco

On Fri, Nov 14, 2008 at 2:40 PM, Gustavo Seabra
<gustavo.seabra_at_gmail.com> wrote:
> Hi Francesco,
>
> I'm sorry i got a bit confused with all the inputs... At which point
> exactly does the Cl- ion start to drift? Is it as soon as you start
> MD, or only when you add nrespa=2? (none of your inputs have this).
>
> Gustavo.
>
> On Thu, Nov 13, 2008 at 10:06 AM, Francesco Pietra
> <chiendarret_at_gmail.com> wrote:
>> Hi:
>> I have carried out docking of a small protein against a large one, the
>> latter generated with Modeller from an extremely similar natural
>> protein and carrying chloride anion ligands. These were accounted for
>> during docking, and in fact they conserved their position after
>> docking. The docking region does not involve the chloride anions
>> directly.
>>
>> With Amber 10 and pmemd, the complex was first minimized under GB conditions:
>>
>> &cntrl
>> imin=1,
>> maxcyc=3000,
>> ncyc=1500,
>> ntb=0,
>> igb=5,
>> cut=999
>> /
>>
>>
>> Then it was heated gradually to 300K and further equilibrated as follows::
>>
>> &cntrl
>> imin=0, irest=0, ntx=1, ntb=0,
>> igb=5, ntc=2, ntf=2,
>> ntt=3, gamma_ln=2.0,
>> nstlim=2500, dt=0.001,
>> ntpr=100, ntwx=100,
>> tempi=100.0, temp0=150.0,
>> cut=999.0, rgbmax=999.0,
>> nmropt=1
>> /
>> &wt TYPE='TEMP0', istep1=0, istep2=2500,
>> value1=100.0, value2=150.0,
>> /
>> &wt TYPE='END'
>> /
>>
>> &cntrl
>> imin=0, irest=0, ntx=1, ntb=0,
>> igb=5, ntc=2, ntf=2,
>> ntt=3, gamma_ln=2.0,
>> nstlim=2500, dt=0.001,
>> ntpr=100, ntwx=100,
>> tempi=150.0, temp0=200.0,
>> cut=999.0, rgbmax=999.0,
>> nmropt=1
>> /
>> &wt TYPE='TEMP0', istep1=0, istep2=2500,
>> value1=150.0, value2=200.0,
>> /
>> &wt TYPE='END'
>> /
>>
>> &cntrl
>> imin=0, irest=0, ntx=1, ntb=0,
>> igb=5, ntc=2, ntf=2,
>> ntt=3, gamma_ln=2.0,
>> nstlim=2500, dt=0.001,
>> ntpr=100, ntwx=100,
>> tempi=200.0, temp0=250.0,
>> cut=999.0, rgbmax=999.0,
>> nmropt=1
>> /
>> &wt TYPE='TEMP0', istep1=0, istep2=2500,
>> value1=200.0, value2=250.0,
>> /
>> &wt TYPE='END'
>> /
>>
>> &cntrl
>> imin=0, irest=0, ntx=1, ntb=0,
>> igb=5, ntc=2, ntf=2,
>> ntt=3, gamma_ln=2.0,
>> nstlim=2500, dt=0.001,
>> ntpr=100, ntwx=100,
>> tempi=250.0, temp0=300.0,
>> cut=999.0, rgbmax=999.0,
>> nmropt=1
>> /
>> &wt TYPE='TEMP0', istep1=0, istep2=2500,
>> value1=250.0, value2=300.0,
>> /
>> &wt TYPE='END'
>> /
>>
>> Then increased dt!!
>>
>> &cntrl
>> imin=0, irest=0, ntx=1, ntb=0,
>> igb=5, ntc=2, ntf=2,
>> ntt=3, gamma_ln=2.0,
>> nstlim=3000, dt=0.002,
>> ntpr=100, ntwx=100,
>> tempi=290.0, temp0=300.0,
>> cut=999.0, rgbmax=999.0,
>> nmropt=1
>> /
>> &wt TYPE='TEMP0', istep1=0, istep2=600,
>> value1=290.0, value2=300.0,
>> /
>> &wt TYPE='END'
>> /
>>
>>
>>
>> As EPTOT ETOT EKTOT were very nearly constant and the whole complex
>> had not suffered visible distotion, I tried MD of this huge,
>> unabridged complex under GB conditions in very small chunks as
>>
>> Production under GB conditions
>> &cntrl
>> imin=0, irest=1, ntx=5, ntb=0,
>> igb=5, ntc=2, ntf=2,
>> ntt=3, gamma_ln=2.0,
>> nstlim=3000, dt=0.002,
>> ntpr=100, ntwx=100,
>> tempi=300.0, temp0=300.0,
>> cut=999.0, rgbmax=999.0
>> /
>>
>>
>> Starting from production 2, I added nrespa=2 (reaching the guard limit
>> of 4femtosec)
>>
>> Surprisingly (for me) the chloride anions started to leave the
>> protein, while no other distortion showed up. While at frame 0 the
>> chloride anions are their positions, at frame 50(a base some 25 ps of
>> trajectory) they are out of the proteins a gradually they disappear
>> from the screen. Evaluating rmsd with ref frame 0, rmsd increases
>> linearly with frame number, and in the attached plot. The minimum
>> potential energy remains at frame 100, out of 250 frames, and ETOT
>> (black), EPTOT (green), and EKTOT (red) seem OK as in the attached
>> plot. Nonetheless, might the large nrespa=2 be responsible for the
>> instability of chloride anion ligands? The size of the system is such
>> that the 50% gain with nrespa=2 is difficult to renounce to.
>>
>> Chloride anion was set as Cl- and xleap did not complain about.
>>
>> Sorry if I made a long story for something trivial, obvious to
>> experienced people.
>>
>> Thanks for any kind of comment
>> francesco pietra
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