AMBER Archive (2009)

Subject: Re: [AMBER] leap and chirality

From: Wei Zhang (
Date: Mon Mar 23 2009 - 13:36:54 CDT

Hi Karl,

     Can you apply the patch I attached and try sleap again?

     NOTE, there is a minor problem with your prep file. There are two
atom with the
same name "H8", you might want to change one of them to some other
name say "H10".



On Mar 23, 2009, at 9:05 AM, Karl Kirschner wrote:

> Hi,
> I have just tried sleap, and obtained the following error message:
> "Error: prep format, sort by first column no longer supported"
> My environmental variables are set to my local ambertools copy, and
> I changed
> leaprc.ff99 to leaprc.ff03. I also check the bugfix page and did not
> see
> anything that pertrains to the above error message. I am pretty sure
> that the
> installation of ambertools was done correctly.
> These prep files were originally outputted by xleap, with minor
> changes made
> to the charge column.
> Cheers,
> Karl
> On Monday 23 March 2009 14:16, David A. Case wrote:
>> On Mon, Mar 23, 2009, Karl Kirschner wrote:
>>> I am having some trouble with the chirality of a nonstandard
>>> reside that I made....
>> One good thing to do would be to download AmberTools1.2, and see if
>> the
>> problem persists with sleap. Wei is working with Matt and Lachele at
>> UGA to try to make the new codes do the right thing here.
>> Of course, this doesn't fix tleap, but I'm not sure who will have the
>> time or energy to do that.
>> ...dac
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