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

From: sugino tatsuro <>
Date: Tue, 16 Jan 2007 10:40:32 +0900

Thank you very much for your advices.

>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?
>How did you distinguish the one atom to be perturbed from the others?
>(A different unit name?)

I looked at the inside of the file by using 'rdparm' to see bond
information. Although perturbed water molecule had no bonds, all the other
water molecules did.
And I distinguished
perturbed one by using VMD and looked it by using movie implemented in VMD.

Here, topology and coordinate files were established 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

I renamed the residue name of the perturbed water / ligand molecules, but
the bonds inside the molecules were not formed; I don't understand what
occurs in the process of the file generation, in which TIP5P water was used
for the water model (in the case of TIP3P, no problems occur).
How can I make bonds among perturbed atoms when TIP5P water model was used?

Any advices are welcome. Thank you very much in advance.

best wishes,

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Received on Wed Jan 17 2007 - 06:08:03 PST
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