AMBER Archive (2005)

Subject: Re: AMBER: about run time in GB and PB

From: Yong Xu (yxu_at_mail.sioc.ac.cn)
Date: Fri Apr 22 2005 - 03:19:05 CDT

thank you, Phin

I use carnal to analysis rmsd by fit protein-mainchain atom. I also
extract pdb structure from MD traj, what I can see is that the ligand
still bind in some residues at the binding pocket, but other part of
protein crash.

yes, I will do test following GB-tutorial.
restraint maybe one alternative.

Yong

> Dear Yong Xu,
>
> did you perform a short energy minimisation of the system before heating
> and equilibrating at 300K?
>
> Have you actually _looked_ at the simulation to see what is going on?
> You might have just forgotten to
> remove the translational/rotational motion before calculating the rmsd,
> or, if you are referring to the rmsd of
> the complex, then maybe the ligand is moving away from the protein, and
> one might need some restraints to
> hold this... but you are only going to know what's going on if you set
> ntpr=1 and look at the simulation at each step
> to see where you are having problems... ptraj will give you the rmsd,
> but it won't tell you where your problems are.
>
> By the way, have you looked at the tutorials available at the amber
> website? They provide examples of
> running MD simulations in explicit or implicit solvent, and also on how
> to analyse the trajectory.
> Maybe you could follow their example, using your protein, rather than
> the protein-ligand complex to see if you can get
> a stable trajectory for just the protein first....
>
> with best regards,
> Phin.
>
>
> Yong Xu wrote:
>
>>Dear Prof. Duan and Phineus
>>
>>thank you for all your reply.
>>I re-evaluated the time need for MD.
>>the information shown in my previous mail is the heating process .
>> During that process, I use position constraint to mainchain. when I
>> run production MD, I loose all atom. the speed of MD is about 1/5-1/4
>> comparing with GB method.
>>
>>another problem arising.
>>when I release all atoms without restraint, the RMSD of whole protein
>> reach to 4-6 angstrom within 60ps. that is to say, the whole system
>> crash.
>>
>>should I restraint something again, like Ca or mainchain?
>>is it correct to analysis result using traj with distance-restraint,
>> angle-restraint, or position constraint for some atoms?
>>
>>Yong
>>
>
>
>>
>
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* State Key Lab of Bioorganic & Natural Product Chemistry *
* Shanghai Institute of Organic Chemistry *
* Chinese Academy of Science *
* 354 Feng Lin Road, Xu Hui District *
* Shanghai, 200032, China *
* Email: yxu_at_mail.sioc.ac.cn *
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