AMBER Archive (2005)

Subject: Re: AMBER: Cyclohexane solvent Box

From: Brent Krueger (kruegerb_at_hope.edu)
Date: Mon Oct 17 2005 - 09:59:44 CDT

Ross,

Hey I am realizing that I never wrote you back about all your job
stuff. Have you made a decision already?

In the very risky chance that you have made a decision, I will still
give a very quick opinion (dept meeting in 4 minutes)

I say go for it. Why not make good money now and live in a cool area
with the chance of making huge money. (Keeping in mind that you are
doing interesting work the whole time -- it wouldn't be worth it if
you job sucked for some reason.) If this company does go down the
tubes in 5 years, you've still got great job experience and I don't
think there would be a problem getting back in academia as long as
you have been able to maintain research activity (even if you don't
publish much). Plus you'd get to live in Canada and see the Bush-
driven demise of the US from someplace else.

Demographics says that the big universities will be hiring science
faculty regularly for the foreseeable future. So, I don't think the
job market will dry up anytime in the next 20 years.

Cheers,
Brent

Oh, could you put the latest AMBER9 on caffeine for me?

On Oct 17, 2005, at 10:03 AM, Ross Walker wrote:

> Dear Andy,
>
>
>> I output the .rst to pdb file, but the cyclohexane molecule
>> is disperse. If
>> i read back into Leap, this is what happen. I have 117 residues. It
>> complaint the atoms are not in residue templates. And if I edit the
>> molecules, I only see boxes and it is without charges.
>> Creating new UNIT for residue: INT sequence: 117
>> Created a new atom named: C1 within residue: .R<INT 117>
>>
>
> Did you build a library file for the residue named INT? In this
> case your
> cyclohexane? If you did then you need to load this into Leap before
> you load
> the pdb file that contains your cyclohexane solvent. It will then
> recognise
> the residue and give it the correct atom types and topology. Also,
> check
> that the name of the residue in the pdb file matches the residue
> name you
> used when you created the unit in the first place.
>
> If you didn't create a library file for it then you need to do this
> first
> before you can load the solvated pdb.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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>
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__________________________________________________________________
Brent P. Krueger phone: 616 395 7629
Assistant Professor fax: 616 395 7118
Hope College
Department of Chemistry
Holland, MI 49423

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