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blubbi Offline OP
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Hi CHARMm users,

I build a system which contains RNA, protein and a membrane with Cholesterol so i need to read in the parameter files for all of the four components (NA, PROT, LIPID, CHOL).

I checked each structure by its own and made sure each works.
But I failed at the point where I want to put the system together. I couldn't manage to read all the required rtf/prm files.

I tried different combinations and orders but no success.
See an example below:

Code:
! Read topology and parameter files
open read card unit 10 name para/top_all27_prot_na.rtf
read  rtf card unit 10

open read card unit 20 name para/par_all27_prot_na.prm
read para card unit 20

open read card unit 10 name para/top_all27_lipid.rtf
read  rtf card append unit 10 

open read card unit 20 name para/par_all27_lipid.prm
read para card append unit 20


stream para/toppar_all27_lipid_cholesterol.str


Before I start to post all possible errors I collected I would like to ask if this is the proper way of reading multiple rft/prm files. If not, please let me know how to read all the needed parameters (NA, PROT, LIPID, CHOLESTEROL)

Kind regards
Bjoern

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rmv Online Content
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A good question for the Parameter forum, and a topic which may have been discussed there before. There's also a post there about the new "all36_lipid" files, which I recommend over either "all27_lipid" (worst choice) or "all32_lipid" (alkanes better).

In brief, the above won't work with the current structure of the RTF and PARAM files (a revision is planned). You must manually combine the RTF files, taking care to avoid duplicate atom numbers and names in the MASS statements, and duplicate residues. I suggest adding the "all36_lipid" files to the "all27_prot_na" files as the best and easiest pathway. For the PARAM files, you should combine each section, i.e. add lipid BOND terms to existing BOND section, etc.


Rick Venable
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Originally Posted By: blubbi
Hi CHARMm users,
You're in the wrong place. This is the CHARMM forum! grin



To solve your problem, you have to renumber the MASS statements in the topology file, copy-paste them into a new "ATOM" section in the parameter file, and read the resulting parameter files with the flex keyword. Please read this discussion thread carefully (including the second page) for a discussion on the subject.

We're currently in the process of reorganizing the CHARMM force field distribution. All the force fields will have non-overlapping MASS numbers and will be compatible with the flexible parameter reader. That should make these kind of annoyances a thing of the past. We're planning to release the new CHARMM force field distribution next week.

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blubbi Offline OP
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Thanks for your replies, I appreciate it very much.

I had the apprehension that it would be the way you wrote.

Since my parent simulation was run with all27_lipid I rather stick with this, shouldn't I?
If not, I'll see if we can purchase the latest CHARMM ;-) version when it got release to get my hands on the new forcefield files and avoid messing around with these.

Meanwhile I'll try to combine all27_prot_na and all27_lipid.

Thanks a lot!

Cheers
Bjoern

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blubbi Offline OP
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Just wanted to let you know that merging all27_prot_na and all27_lipid (rtf and prm) worked.

Wasn't that much hassle.

Thanks again!

Cheers
Bjoern

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rmv Online Content
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The force field files can be downloaded by anyone from the MacKerell lab site.


Rick Venable
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blubbi Offline OP
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Originally Posted By: rmv
The force field files can be downloaded by anyone from the MacKerell lab site.


Ah, good to know, thanks for the info.


I realized that I used top_all27_prot_lipid to setup the membrane and since O3 referes to OHL in toppar_all27_lipid_cholesterol and OHL is type 165 in top_all27_prot_lipid I think I have found the mistake.

I'll try to append the all27_na to all27_prot_lipid and regenerate the RNA psf from the PDB (or change types... python will come i handy here)

Cheers
Bjoern

Last edited by blubbi; 06/29/10 03:49 PM.
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Originally Posted By: blubbi
So please ignore the stuff below - for the moment - wink
Why don't you just edit your post and cut-and-paste the stuff "to be ignored" to a text file on your desktop? That would prevent people from stumbling across it while using the search function and getting confused. It's a question of keeping the noise down. wink
But do it fast, because the "edit" function gets automatically disabled after a number of hours.

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blubbi Offline OP
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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, 559 downloads)
top_all27_prot_lipid_na.rtf.txt (627.73 KB, 469 downloads)
regen.log.txt (12.23 KB, 442 downloads)
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It's just a copy-paste error. In your parameter file, you have an "IMPROPER" section, then a "CMAP" section, and then a bunch of loose improper definitions that CHARMM cannot process because they're in the CMAP section...

It probably would have taken you less time to analyze the error message and find the problem by yourself than to dump all this stuff on the CHARMM forums. Not to mention the time we would have saved, and the missed opportunity to practice your problem-solving skills. More on that topic in my problem solving 101 rant.

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