AMBER Archive (2006)

Subject: Re: AMBER: Question about renaming a residue

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Feb 17 2006 - 20:05:37 CST

Dear Kara,

It should not be that hard. What kind of a library file do u have that
xleap recognizes these structures? Are the .lib file or .prep file? I
would change all of the 'old' residue naming (which is UNK) to a new one,
and save the file. And when u load those structures in xleap again, they
will be seen in the new residue names.

For instance, I just saved the residue 'RG' in a .lib file format. In all
entry lines, u will see the name of the residue in it, such as;

!!index array str
 "RG"
!entry.RG.unit.atoms table str name str type int typex int resx int
flags int seq int elmnt dbl chg
 "P" "P" 0 1 131072 1 15 1.166200
 "O1P" "O2" 0 1 131072 2 8 -0.776000
 "O2P" "O2" 0 1 131072 3 8 -0.776000
.
.
.
 "HO'2" "HO" 0 1 131072 33 1 0.418600
 "O3'" "OS" 0 1 131072 34 8 -0.524600
!entry.RG.unit.atomspertinfo table str pname str ptype int ptypex int
pelmnt dbl pchg
 "P" "P" 0 -1 0.0
 "O1P" "O2" 0 -1 0.0
 "O2P" "O2" 0 -1 0.0
.
.
.
"HO'2" "HO" 0 1 131072 33 1 0.418600
 "O3'" "OS" 0 1 131072 34 8 -0.524600
!entry.RG.unit.atomspertinfo table str pname str ptype int ptypex int
pelmnt dbl pchg
 "P" "P" 0 -1 0.0
 "O1P" "O2" 0 -1 0.0
 "O2P" "O2" 0 -1 0.0
.
.
.

So, changing all these 'RG's into a new residue will change the name of
this residue.

If the file is in .prep format, it will look like the following:

 0 0 0

 leap-generated prep residue
RG.res
RG INT 0
CHANGE NOMIT DU BEG
   0.00000
.
.
.

Again, changing the word 'RG' to a new file will change the residue name
for this structure.

Good luck,

On Fri, 17 Feb 2006, Kara Di Giorgio wrote:

> I've created two different residues in the past and they were both
> called UNK. I didn't think about it as they were not used at the same
> time. However, now I DO want to use them as part of the same
> simulation. How would I change the name of one of them in such a way
> that xLeap recognizes them as different. I've tried re-naming things
> in the past, but the original name seemed to stay as part of it. Was I
> incorrect? How would you suggest going about this? (Just re-creating
> one of the residues as something other than UNK isn't an easy option as
> they were difficult to set up in the past.)
>
> Any help would be greatly appreciated.
>
> Thanks,
>
> Kara Di Giorgio
> University of the Pacific
>
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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