Re: [AMBER-Developers] Attn: sleap developer(s) - doesn't like solvateCap?

From: Ben Roberts <>
Date: Wed, 17 Mar 2010 11:08:46 -0400

Hi Wei,

On 16/3/2010, at 9:45 p.m., Wei Zhang wrote:

> Sorry I missed you previous message.

That's OK. It seems the problem I reported there has been solved in
sleap by now , else the script I'm mentioning now would not work even
as far as it does. (My problem then concerned a problem with metal ion
type handling.)

> Would you please send me your input and script?

For the sake of not sending large emails or having them defanged, I've
put the material online.

See here:

You'll need all the files in that directory, I believe.

Then, LeAP (whether sleap or tleap) can be run by:

<program> -f 1FWJ_high.leaprc

However, the culprit line is at the end of 1FWJ_middle.leaprc, which is
sourced by 1FWJ_high.leaprc.

Let me know if you have any more questions or can't access the material.


> On Mar 16, 2010, at 7:48 PM, Ben Roberts wrote:
>> Hi all,
>> Not sure if this list is the correct place for this - but since when
>> a few weeks ago I posted an sleap/tleap difference to the main Amber
>> list it got no response, I'm trying here. If this isn't the right
>> place, I'd appreciate any pointers as to where to go.
>> Anyway, I'm trying to put a sphere of water around a particular atom
>> using LeAP. When I try the following in sleap, though, it doesn't
>> complain - it just does nothing.
>> solvateCap model TIP3PBOX model.770.O 20
>> rgn size: 40.000 40.000 40.000
>> svt size: 18.774 18.774 18.774
>> nx,ny,nz: 3 3 3
>> [gtkleap]$
>> And then it writes out the output, which contains no water other than what
>> was already present.
>> In the same vein, if I try to use a LIST of ATOMs, as the documentation
>> implies I can do, I get a negative response:
>> solvateCap model TIP3PBOX { model.1.NI model.2.NI } 20.0
>> Error: can not understand mask { model.1.NI model.2.NI }
>> Your thoughts?
>> Cheers,
>> Ben

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Received on Wed Mar 17 2010 - 08:30:05 PDT
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