AMBER Archive (2005)

Subject: Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Nov 15 2005 - 22:43:09 CST

Dear DAC,

I am getting the same error what Nithin is getting. Here is what I have
done and the error I am getting:

[yildirim_at_anatolia ~/nithin]# ls -l
total 68
-rw-r--r-- 1 yildirim users 16271 2005-11-15 23:37 leap.log
-rw-r--r-- 1 yildirim users 6284 2005-11-15 23:35 popc.frcmod
-rw-r--r-- 1 yildirim users 20933 2005-11-15 23:35 popc.pdb
-rw-r--r-- 1 yildirim users 10380 2005-11-15 23:35 popc.prepin
-rw-r--r-- 1 yildirim users 134 2005-11-15 23:37 test.in
-rw-r--r-- 1 yildirim users 225 2005-11-15 23:37 test.in~

[yildirim_at_anatolia ~/nithin]# more test.in
source leaprc.ff94
loadAmberPrep popc.prepin
loadAmberParams popc.frcmod
x = loadPdb popc.pdb
edit x
saveAmberParm x prmtop prmcrd

[yildirim_at_anatolia ~/nithin]# xleap -f test.in
-I: Adding /programs/amber8/dat/leap/prep to search path.
-I: Adding /programs/amber8/dat/leap/lib to search path.
-I: Adding /programs/amber8/dat/leap/parm to search path.
-I: Adding /programs/amber8/dat/leap/cmd to search path.
-f: Source test.in.
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 140
!FATAL: Message: Atom named C67 from POP did not match !
!
!ABORTING.
[yildirim_at_anatolia ~/nithin]#

I used the files sent by Nithin (popc.frcmod, popc.pdb, popc.prepin). The
test.in has the same procedure u described. The error I am getting is same
as Nithin's. My operating system is SUSE Linux 9.1 and the machine has a
P4-3.4 GHz CPU. I am using AMBER 8 while testing this problem.

Best,

On Mon, 14 Nov 2005, David A. Case wrote:

> On Fri, Nov 11, 2005, Nitin Bhardwaj wrote:
>
> > Thanks fo replying again. The lipids are not close to each other. I
> > created the second lipid by copying the first lipid and moved the
> > second away along the x-axis by 8 Ang. So they are approx 8 Ang away.
> > And the atoms that are being connected are ~9 Ang away. C67 is present
> > in the structure. Its the second last carbon in the longer tail of the
> > lipid.
> >
> >
> > I am at my wit's end.
>
> So am I, since I can't reproduce the behavior you are seeing. Just to be
> clear, here is what I did:
>
> source leaprc.ff94
> loadAmberPrep popc.prepin
> loadAmberParams popc.frcmod
> x = loadPdb popc.pdb (the version with two lipids)
> edit x (to confirm that there are no bonds bewteen the two lipids)
> saveAmberParm x prmtop prmcrd
>
> There is nothing funny around atom C67, no bonds between the two lipids, etc.
> There were no errors or messages about superimposing torsions.
>
> What compiler and OS are you using? Do you have access to any other sort
> of machine that could be used to see if this is an architecture problem we
> haven't run into before?
>
> ...regards...dac
>
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
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  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
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