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From: sxzheng <sxzheng_at_mail.shcnc.ac.cn>

Date: Sat 12 Jan 2002 11:21:30 +0800

Jose Ramon Blas

It's very kindful for your response.

The problem I found can only use the electrostatic decoupling and slow growth for calculating the vdw energy method to resolve.

I have one ligand with one positive charge and a receiptor with eight negative charges to calculate the absolute free energy.

Then in water solution the system has one positive charge and zero perturbed charge and complex system has 7 negative charge and 8 negative perturbed charge.

Can you give me some advice on neutralize the system.

Should I neutralize the water solution system? If I don't neutralize the water solution system should I addions to make the complex system has zero or one positive charge?

If I use "addions unit Na+ 0" to nertralize the complex system it only adds 6 Na+ then the system has also one negative charge.Should I use "addions unit Na+ 7" to neutralize the system absolutely or "addions unit Na+ 8" to make the system has one positive charge to equil the total charge with the water solution system while not neutralize the water solution system.

Can you give me some advice ?

Best regards

zsx

ÔÚ 02-1-7 2:33:00 ÄúÐ´µÀ£º

*>Hi,
*

*>I do not know if anyone has answered your question in the AMBER list.
*

*>I came just this morning from holidays.
*

*>
*

*>You may have a problem with the velocities of some atoms. Usually this
*

*>error appears
*

*>when two atoms are clashing. Try to find which atoms could be and reset
*

*>their coordinates
*

*>and/or initial velocities. The system will reach equilibrium very soon,
*

*>less than 5 ps.
*

*>
*

*>Hope this helps,
*

*>
*

*>Blas
*

*>
*

*>--
*

*>
*

*>----------------------------------------------------------------
*

*>----------------------------------------------------------------
*

*>
*

*>J.R. Blas
*

*>
*

*>Grup de RECONEIXEMENT MOLECULAR | e-mail:jramon_at_borzoi.bq.ub.es
*

*>Dept.Bioquimica i Biol.Molecular | phone: + 34 93 403 58 58
*

*>Facultat de Quimica | FAX: + 34 93 402 12 19
*

*>Universitat de Barcelona |
*

*>Marti i Franques,1 |
*

*>08028 Barcelona |
*

ÖÂ

Àñ£¡

sxzheng

sxzheng_at_mail.shcnc.ac.cn

Received on Fri Jan 11 2002 - 19:21:30 PST

Date: Sat 12 Jan 2002 11:21:30 +0800

Jose Ramon Blas

It's very kindful for your response.

The problem I found can only use the electrostatic decoupling and slow growth for calculating the vdw energy method to resolve.

I have one ligand with one positive charge and a receiptor with eight negative charges to calculate the absolute free energy.

Then in water solution the system has one positive charge and zero perturbed charge and complex system has 7 negative charge and 8 negative perturbed charge.

Can you give me some advice on neutralize the system.

Should I neutralize the water solution system? If I don't neutralize the water solution system should I addions to make the complex system has zero or one positive charge?

If I use "addions unit Na+ 0" to nertralize the complex system it only adds 6 Na+ then the system has also one negative charge.Should I use "addions unit Na+ 7" to neutralize the system absolutely or "addions unit Na+ 8" to make the system has one positive charge to equil the total charge with the water solution system while not neutralize the water solution system.

Can you give me some advice ?

Best regards

zsx

ÔÚ 02-1-7 2:33:00 ÄúÐ´µÀ£º

ÖÂ

Àñ£¡

sxzheng

sxzheng_at_mail.shcnc.ac.cn

Received on Fri Jan 11 2002 - 19:21:30 PST

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