Re: AMBER: perturbed atoms are not bonded on using TIP5P water

From: sugino tatsuro <>
Date: Tue, 16 Jan 2007 12:19:59 +0900

Dear David,


Thank you very much for your kind advices. In addition to my previous

e-mail, I would like to add some information of my status, since mu

colleagues advised me to provide more intimate information of my problems.

I am very sorry for your confusing, but please see this e-mail, in stead of

the previous one.


>How did you establish this? Were you looking inside the prmtop file to

>see that the perturbed water had no bonds, but all the others did?


Before saving the file, I confirmed information of the molecular

topology (also for a perturbed water molecule) in my system, by using 'desc'

command in xLeaP. Then, I saved the file with the saveAmberParmpert

command in xLeaP.


Next, I looked at the inside of the file with the use of 'rdparm' to

molecular topology, and knew that the perturbed water molecule did not hold

bonds, whereas all of the other water molecules did hold the bond


>How did you distinguish the one atom to be perturbed from the others?

>(A different unit name?)


For the perturbed water molecule I renamed its residue name, but the bonds

the molecules were not formed; I don't understand what occurs in the process
of the

file generation, when TIP5P water model was used (in the case of TIP3P, no



In addition, I attempted perturbation for a ligand molecule with the TIP5P
water model

for bulk water. Also in those cases, for lignad molecule, bond information
did not hold.

So, it seems that, when TIP5P model is included in the system analyzed, such
an error

(= disappear of the topology information for the perturbed molecules)


If you would tell me how I can make bond information for the perturbed
molecule in the

case of including TIP5P water model, I would much appreciate it.


Here, topology and coordinate files were made by using the following

> loadamberparams gaff.dat

> source TIP5P.cmd

> loadamberparams parm99EP.dat

> loadamberparams frcmod.tip5p

> model = TP5

> solvatebox model TP5 20

> edit model ( and select a water molecule and set perturbation by GUI )

> saveamberparm model parmpert.crd


Thank you very much in advance.


best wishes,


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Received on Wed Jan 17 2007 - 06:08:05 PST
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