Quoting Bill Ross <ross.cgl.ucsf.EDU>:
>> >> But I found the carbon atoms are moving a lot
>> >
>> > What kind of movement? (I see you are using constant volume, so
>> > coordinate scaling would not be involved as it would be for
>> > constant pressure.)
>> >
>> The six membered-like rings doesn't exist even though the actual
>> monomer is the two carbon molecule.
>
> You won't see bonds that aren't there. But this has no bearing
> on the type of movement. You are implying the sheet is becoming
> distorted, but it sounds like the problem is that you expect
> nonexistent bonds to be displayed in some viewing program?
>
I just expected all the two-carbon residues are on the plain not distorted.
> Why have a 2-carbon basic residue rather than a ring?
>
Becuase I failed to generate prepi by using antechamber with more than
two-carbon monomer.
>> ##bondByDistance gr 1.5
>
> This explains how you got the long bonds. An alternative is to
> use the 'bond' command in leap to set each bond. However, it seems
> bondByDistance should have worked, and this may be worth debugging
> for whoever is maintaining leap.
>
If I simply use 'bond' command, I need to specify all atom numbers.
But I have more than 2000 carbon atoms finally and there is no way to
pair carbon indices.
Thank you.
Bongkeun Kim
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Received on Wed Oct 20 2010 - 14:00:07 PDT
