AMBER Archive (2005)

Subject: RE: AMBER: An atom name with 4 characters is not compatible with Leap ?

From: Arnoult, Eric [PRDFR] (EArnoult_at_prdfr.JNJ.com)
Date: Wed Jul 27 2005 - 02:20:27 CDT

Dear Dr Case,

I completed my last question.

Can you try this leap.in ?

"source leaprc.ff03

source leaprc.gaff

loadAmberPrep test_prp_resp.in

lig = loadPdb test.mpdb

saveAmberParm lig test.top test.crd

quit"

 

I attached to this mail the prep file, and the mpdb file

 

can you give me you advise about it ?

Many thanks

éric

 

-----Original Message-----

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu]On Behalf

Of David A. Case

Sent: Friday, July 22, 2005 7:28 PM

To: amber_at_scripps.edu

Subject: Re: AMBER: An atom name with 4 characters is not compatible

with Leap ?

 

On Fri, Jul 22, 2005, Tim Meyer wrote:

>

> the problem comes from the pdb format. columns 13,14,15,16 contain atom

> name, however 14 is supposed to contain the element character so CL29

> doesn't fit.

This is not quite correct. The pdb standard says the the atomic symbol
should

be right justified in columns 13 and 14. So "CL29" would fit fine in columns

13-16. At I indicated in an earlier mail, I think the problem is somewhere

else, and just appears to be related to four-character names.

...dac

 

 


  • application/octet-stream attachment: test.mpdb

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