Originally Posted By: Kenno
But do it fast, because the "edit" function gets automatically disabled after a number of hours.

Done

Sadly the above didn't work. I merged the all27_na with all27_prot_lipid, removed all duplicates but when re-creating my PSF from a PDB I get some errors which I can't identify but which for sure result from an error in my prm/rtf files.

I pasted the prm/rtf files here: http://paste.pocoo.org/show/231347/ (scroll down to line 5371 for top_all27_prot_lipid_na)
or find them attached to this post.

The part where I added the NA stuff is marked with
!!!!NA_START!!!! and !!!!NA_STOP!!!!

And here's the error (or find regen.log attached to this post):
http://paste.pocoo.org/show/231350/

A short excerpt from the log:
Code:
[...]
          PARAMETER FILE BEING READ FROM UNIT 20
 TITLE> *>CHARMM22 ALL-HYDROGEN PARAMETER FILE FOR PROTEINS AND LIPIDS <<
 TITLE> *>>>>> INCLUDES PHI, PSI CROSS TERM MAP (CMAP) CORRECTION <<<<<<<
 TITLE> *>>>>>>>>>>>>>>>>>>>>>>   JULY, 2003   <<<<<<<<<<<<<<<<<<<<<<<<<<
 TITLE> * ALL COMMENTS TO ADM JR. VIA THE CHARMM WEB SITE: WWW.CHARMM.ORG
 TITLE> *               PARAMETER SET DISCUSSION FORUM
 TITLE> *
WARNING from DECODI -- Zero length string being converted to 0
 PARRDR> WARNING: ATOMS IN PHI1 (CMAP) HN2  X    X    NN2   DONT EXIST
[...]
 PARRDR> NOTE: atom type "HT  " is removed from previous group
 PARRDR> NOTE: atom type "OT  " is removed from previous group
*****  WARNING  ***** PARRDR no nonbond parameters for atom type: 250  POLO
 NO nonbond interactions will be computed for this atom type.
PARRDR:   IATVDW   38
PARRDR:   NATVDW  192
PARRDR:      NBC   20   21   32   33   39   40   37   29   30   31
                   34   35   25   26   36   27   38   41   22   23
[...]
PARRDR:     NATC  334
PARRDR:      ITC   27   32   28  122   33   31   34   35   36   37
                   29   30   39   40   41   85   86    0    0    1
[...]
      ***** LEVEL -3 WARNING FROM <PARRDR> *****
      ***** Null nonbond group found. Redo.
      ******************************************
      BOMLEV (  0) IS REACHED - TERMINATING. WRNLEV IS  5



this is my input file (just in case):
Code:
*Regenerate RNA because it was build with the standard parameter
*files and thus the MASS (type) of atoms do not match
*

open read card unit 10 name ../para/top_all27_prot_lipid_na.rtf
read  rtf card unit 10

open read card unit 20 name ../para/par_all27_prot_lipid_na.prm
read para card unit 20

open read card unit 10 name ../input/rna.pdb
read sequence pdb unit 10
generate RNAA setup warn first 5TER last 3TER

open read card unit 10 name ../input/rna.pdb
read coor pdb  unit 10 resid

!Print heavy atoms with unknown coordinates
coor print sele ( .not. INIT ) .and. ( .not. hydrogen ) end

ic param
ic build
prnlev 0
hbuild
prnlev 5

open write card unit 10 name rna.pdb
write coor pdb  unit 10 

open write card unit 10 name rna.crd
write coor unit 10 card

open write unit 10 card name rna.psf
write psf  unit 10 card

open write unit 10 card name rna.xplor.psf
write psf  xplo unit 10 card

stop


Does anyone have an Idea where I messed up?

Attached Images
par_all27_prot_lipid_na.prm.txt (260.28 KB, 567 downloads)
top_all27_prot_lipid_na.rtf.txt (627.73 KB, 476 downloads)
regen.log.txt (12.23 KB, 449 downloads)