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.scripps.edu [mailto:owner-amber.scripps.edu]On Behalf
Of David A. Case
Sent: Friday, July 22, 2005 7:28 PM
To: amber.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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
- application/octet-stream attachment: test.mpdb
Received on Wed Jul 27 2005 - 08:53:00 PDT
