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About CHARMM General Force Field
#24178 05/05/10 07:23 AM
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I am reading in the topology and parameter files using the way described in http://mackerell.umaryland.edu/Warning.html. So my input file was just:

==========input=============================
bomblev 0

open read form unit 11 name top_all22_prot.inp
read rtf card unit 11
close unit 11

open read form unit 12 name par_all22_prot.inp
read parameter card unit 12
close unit 12

open read form unit 13 name top_all36_cgenff.rtf
read rtf card append unit 13
close unit 13

open read form unit 14 name par_all36_cgenff.prm
read parameter card append unit 14
close unit 14

stop

============================================

But I got error messages:


=============errors=========================
CHARMM> open read form unit 13 name top_all36_cgenff.rtf
VOPEN> Attempting to open::top_all36_cgenff.rtf::
OPNLGU> Unit 13 opened for READONLY access to top_all36_cgenff.rtf

CHARMM> read rtf card append unit 13
MAINIO> Residue topology file being read from unit 13.
TITLE> * -------------------------------------------------------------------------- *
TITLE> * CGENFF: TOPOLOGY FOR THE CHARMM GENERAL FORCE FIELD V. 2B4 *
TITLE> * FOR SMALL MOLECULE DRUG DESIGN *
TITLE> * -------------------------------------------------------------------------- *
TITLE> *
*** WARNING **** residue ALAD already exists (old one deleted)
RESI ALAD 0.00
*** WARNING **** residue GLYP already exists (old one deleted)
RESI GLYP -1.00
IN USE MAXIMUM
ATOMS 10003 10000
BONDS 9534 10000
ANGLES 2 10000
DIHEDRALS 0 10000
IMPROPERS 496 4000
CROSSTERMS 27 2000
EXCLUSIONS 0 5000
ACCEPTORS 221 600
DONORS 141 600
BUILD/IC 8809 10000

***** LEVEL -4 WARNING FROM <RTFRDR> *****
***** LIMIT EXCEEDED
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5


============================================


May I ask how I should read in the CGFF correctly?

And I found the file below in the tutorialL
tutorial.html

Is this the introduction of how the CGFF was generated, or is this teaching us how to correctly read in the CGFF together with the protein force field (all22)?

Thanks a lot!

Last edited by mooctopus; 05/05/10 07:28 AM.
Re: About CHARMM General Force Field
mooctopus #24182 05/05/10 04:56 PM
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About the "limit exceeded": this is numero uno on the CGenFF FAQ and I answered it numerous times on these forums.

About the "residue already exists (old one deleted)" warnings: although these are harmless in most cases, I probably should either remove the residues involved from the CGenFF distribution, or update the recommendation to first stream in CGenFF and then the bio force field(s). I'm still debating what's best.

Re: About CHARMM General Force Field
Kenno #24183 05/05/10 06:37 PM
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Thank you, Kenno!
You posted on the webpage that where "gnu" and "medium" should be modified according to architecture and desired CHARMM size, resp. Version 34b2 can be compiled by cd-ing into your c34b2 directory and untarring this file before compilation (this will overwrite ./install.com, ./source/fcm/dimens.fcm and ./doc/preflx_list.doc). Older CHARMM version are not supported. Be advised that the CHARMM build system will not recompile affected modules after changing preprocessor settings! Because of this, you cannot recompile CHARMM with CGenFF support in a directory in which you previously compiled CHARMM without CGenFF support unless you do

I am using c34b1, and I did not succeed in compiling this CGenFF. Is that because the version was older?

Thank you!

Re: About CHARMM General Force Field
mooctopus #24184 05/05/10 06:53 PM
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Hi Kenno, I guess c34b1 is not enough, since I run just the CGenFF themselves and got the skull message:
CHARMM> bomblev 0

CHARMM>

CHARMM>

CHARMM>

CHARMM> open read form unit 13 name top_all36_cgenff.rtf
VOPEN> Attempting to open::top_all36_cgenff.rtf::
OPNLGU> Unit 13 opened for READONLY access to top_all36_cgenff.rtf

CHARMM> read rtf card unit 13
MAINIO> Residue topology file being read from unit 13.
TITLE> * -------------------------------------------------------------------------- *
TITLE> * CGENFF: TOPOLOGY FOR THE CHARMM GENERAL FORCE FIELD V. 2B4 *
TITLE> * FOR SMALL MOLECULE DRUG DESIGN *
TITLE> * -------------------------------------------------------------------------- *
TITLE> *

CHARMM> close unit 13
VCLOSE: Closing unit 13 with status "KEEP"

CHARMM>

CHARMM> open read form unit 14 name par_all36_cgenff.prm
VOPEN> Attempting to open::par_all36_cgenff.prm::
OPNLGU> Unit 14 opened for READONLY access to par_all36_cgenff.prm

CHARMM> read parameter card unit 14

PARAMETER FILE BEING READ FROM UNIT 14
TITLE> * -------------------------------------------------------------------------- *
TITLE> * CGENFF: PARAMETERS FOR THE CHARMM GENERAL FORCE FIELD V. 2B4 *
TITLE> * FOR SMALL MOLECULE DRUG DESIGN *
TITLE> * -------------------------------------------------------------------------- *
TITLE> *

***** LEVEL -3 WARNING FROM <PARRDR> *****
***** Maximum no. of dihedrals reached
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5

Re: About CHARMM General Force Field
mooctopus #24186 05/06/10 12:53 AM
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CGenFF is officially only supported from c35 onwards. I'm offering a patch for c34b2 on my website as a courtesy to c34 users, but it requires recompiling CHARMM, and if you want to use an older version than that, you're on your own. It should not be too difficult to adjust the patch to your CHARMM version but I'm not helping with it.

Last edited by Kenno; 05/06/10 12:57 AM. Reason: More helpful information.
Re: About CHARMM General Force Field
Kenno #24188 05/06/10 06:44 AM
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Okay, I will install c35b then

Re: About CHARMM General Force Field
mooctopus #24190 05/06/10 07:38 AM
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Hi Kenno, thanks a lot! I installed c35b3 and finally it works smile

Re: About CHARMM General Force Field
mooctopus #24191 05/06/10 08:18 AM
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May I also ask how to merge the teamsugar force field with the protein and CGenFF?

Thanks a lot!

Re: About CHARMM General Force Field
mooctopus #24192 05/06/10 04:48 PM
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I guess the Mass number matters? Is that okay if I just remas the atoms?

Re: About CHARMM General Force Field
mooctopus #24193 05/06/10 05:19 PM
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CHARMM internally refers to atom types as integers, which are provided by the MASS statements in the topology (rtf) file. For the purpose of the following discussion, I will call these integers "MASS numbers" (even though it's a bit of a misnomer).
CHARMM has a hard-coded maximum MASS number of 500, and increasing this would make the static memory usage explode, which is bad because CHARMM constantly brushes the maximum static memory allocation on certain architectures. The MASS numbers in CGenFF have a range of 256, those in the carbohydrate FF have a range of 99, and those in the protein force field have a range of 121. 256+99+121=476, so you can renumber the MASS statements by adding a constant offset to the MASS numbers in CGenFF and another constant offset to the carbohydrate force field, but you have to choose those offsets carefully.
Note that these MASS lists are pretty sparse. CGenFF actually only contains 141 atom types, the carbohydrate force field 45, and the protein force field 95. 141+45+95=281, so, if you renumber each and every MASS statement, you can have a contiguous range of MASS numbers from 1-281, leaving plenty of room for other CHARMM force fields. But it's more work, and more prone to breaking the psf (see warning below).
Note that CGenFF uses the flexible parameter reader ("flex" keyword), which requires an ATOMS section in the parameter (prm) file that is a duplicate of the MASS list in the topology (rtf) file.

WARNING: changing the MASS number of an atom type has no physical impact, except that it invalidates any psf file containing that atom type! In other words, you have to re-generate the psf after changing the MASS numbers. This is the reason why the MASS lists are sparse as they are: to allow for future atom types to be inserted without requiring the user to regenerate their psf files.

Last edited by Kenno; 05/06/10 05:24 PM. Reason: Added "more prone to breaking the psf..."
Re: About CHARMM General Force Field
Kenno #24194 05/06/10 05:23 PM
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Thanks! This is very helpful:)

Re: About CHARMM General Force Field
Kenno #24195 05/06/10 07:33 PM
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So I have tried the script below, in which par_all36_cgenff_remas.prm and top_all36_carb_remas.rtf are the sugar ff after renumber the mass index of each atom number.

====== input ==========
open unit 10 read form name top_all22_prot.rtf
read rtf card unit 10 !append
close unit 10

open unit 11 read form name par_all22_prot.prm
read param card flex unit 11 !append
close unit 11

open unit 12 read card name top_all36_cgenff_remas.rtf
read rtf card unit 12 append
close unit 12

open unit 13 read card name par_all36_cgenff_remas.prm
read para card flex unit 13 append
close unit 13


open read form unit 14 name top_all36_carb_remas.rtf
read rtf card unit 14 append
close unit 14

open read form unit 15 name par_all36_carb_remas.prm
read parameter card flex unit 15 append
close unit 15

stop

============================

But there were a lot bond,angle,dihedral information not read in by charmm. The error message is:

==========error message====================
CHARMM> read parameter card flex unit 15 append

PARAMETER FILE BEING READ FROM UNIT 15
TITLE> * $ID: PAR_ALL36_CARB.PRM,V 1.3 2009/06/09 21:49:31 OGUVENCH EXP $
TITLE> *>>>>>>>>>>>> ALL-HYDROGEN PARAMETERS USED IN THE <<<<<<<<<<<<<<<<
TITLE> *>>>>> DEVELOPMENT OF THE CHARMM CARBOHYDRATE FORCE FIELD<<<<<<<<
TITLE> *>>>>>>>>>>>>>>>>>>>>>>>>> JUNE 2009 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
TITLE> *>>>>>>>> DIRECT COMMENTS TO ALEXANDER D. MACKERELL JR. <<<<<<<<<<
TITLE> *>>>>>>>>>> VIA THE CHARMM WEB SITE: www.CHARMM.ORG <<<<<<<<<<<<<<
TITLE> *>>>>>>>>>>>>>>> PARAMETER SET DISCUSSION FORUM <<<<<<<<<<<<<<<<<<
TITLE> *>>>
TITLE> *>>> THIS IS A RELEASE VERSION BASED ON CVS PARAMETERS V 1.110
TITLE> *>>> CURRENT TOPOLOGY AND PARAMETER FILES CAN BE OBTAINED FROM
TITLE> *>>> [url=HTTP://MACKERELL.UMARYLAND.EDU][url=HTTP://MACKERELL.UMARYLAND.EDU][url=HTTP://MACKERELL.UMARYLAND.EDU]HTTP://MACKERELL.UMARYLAND.EDU[/url][/url][/url]
TITLE> *
PARRDR> WARNING: ATOMS IN BOND OC2D CC2O 700.00000 1.21500 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CC2O CC33 330.00000 1.50000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CC2O CC31 330.00000 1.50000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CC2O CC32 330.00000 1.50000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND OC2D CC2O 700.00000 1.21500 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND HCR1 CC2O 330.00000 1.11000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CC2O CC33 250.00000 1.50000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CC2O CC31 250.00000 1.50000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CC31 CC31 222.50000 1.50000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CC31 CC31 222.50000 1.48500 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CC31 CC31 222.50000 1.50000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CC31 CC32 222.50000 1.53800 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CC31 CC32 222.50000 1.48500 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CC30 CC33 222.50000 1.53800 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CC31 CC32 222.50000 1.53800 DONT EXIST

...
================================

I found in the instruction page that http://dogmans.umaryland.edu/~kenno/cgenff/faq.html#compile
we need to do ./install.com gnu medium +CGENFF

and I wonder how if I should conduct similar procedure before I am able to use the team sugar ff.

Thanks a lot!

Last edited by mooctopus; 05/06/10 07:35 PM.
Re: About CHARMM General Force Field
mooctopus #24196 05/06/10 09:26 PM
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  • Stop calling it "team sugar ff". It's the CHARMM carbohydrate force field. "team sugar" was used to refer to the people that parameterized it.
  • The error suggests that you don't have the ATOMS section with MASS records in your carbohydrate parameter file.

Re: About CHARMM General Force Field
Kenno #24197 05/06/10 10:03 PM
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Okay, sorry about that.

Re: About CHARMM General Force Field
mooctopus #24199 05/06/10 10:17 PM
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I have added the atoms in the CGenFF remased parameter file. And now I got the error message below:

======= error message =======
CHARMM> open read form unit 15 name par_all36_carb_remas.prm
VOPEN> Attempting to open::par_all36_carb_remas.prm::
OPNLGU> Unit 15 opened for READONLY access to par_all36_carb_remas.prm

CHARMM> read parameter card flex unit 15 append

PARAMETER FILE BEING READ FROM UNIT 15
TITLE> * $ID: PAR_ALL36_CARB.PRM,V 1.3 2009/06/09 21:49:31 OGUVENCH EXP $
TITLE> *>>>>>>>>>>>> ALL-HYDROGEN PARAMETERS USED IN THE <<<<<<<<<<<<<<<<
TITLE> *>>>>> DEVELOPMENT OF THE CHARMM CARBOHYDRATE FORCE FIELD<<<<<<<<
TITLE> *>>>>>>>>>>>>>>>>>>>>>>>>> JUNE 2009 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
TITLE> *>>>>>>>> DIRECT COMMENTS TO ALEXANDER D. MACKERELL JR. <<<<<<<<<<
TITLE> *>>>>>>>>>> VIA THE CHARMM WEB SITE: www.CHARMM.ORG <<<<<<<<<<<<<<
TITLE> *>>>>>>>>>>>>>>> PARAMETER SET DISCUSSION FORUM <<<<<<<<<<<<<<<<<<
TITLE> *>>>
TITLE> *>>> THIS IS A RELEASE VERSION BASED ON CVS PARAMETERS V 1.110
TITLE> *>>> CURRENT TOPOLOGY AND PARAMETER FILES CAN BE OBTAINED FROM
TITLE> *>>> [url=HTTP://MACKERELL.UMARYLAND.EDU][url=HTTP://MACKERELL.UMARYLAND.EDU][url=HTTP://MACKERELL.UMARYLAND.EDU]HTTP://MACKERELL.UMARYLAND.EDU[/url][/url][/url]
TITLE> *

***** LEVEL -1 WARNING FROM <PARRDR> *****
***** ATOM has the same name as another atom.
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5

=========================

I have compared the parameter files of the protein force field, CGenFF and CHARMM carbohydrate force field, and did not find any atoms exist more than once.

May I ask how I could solve this problem?

Thanks you very much!

Re: About CHARMM General Force Field
mooctopus #24200 05/07/10 12:04 AM
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It may be a CHARMM release version issue, based on the number of characters allowed in the 2 kinds of atom names, the IUPAC type label and the atom parameter name. The c34b1 release might not support the longer names, which would lead to these types of apparent errors.


Rick Venable
computational chemist

Re: About CHARMM General Force Field
rmv #24201 05/07/10 03:52 AM
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I am actually using CHARMM c35b3. So do you think there might be any solutions?

Re: About CHARMM General Force Field
mooctopus #24202 05/07/10 04:29 AM
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Then it is more likely that there's an error in the modified files somewhere, like a duplicate name ...


Rick Venable
computational chemist

Re: About CHARMM General Force Field
rmv #24208 05/07/10 03:57 PM
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Originally Posted By: rmv
The c34b1 release might not support the longer names, which would lead to these types of apparent errors.
The possibility crossed my mind. Especially with these errors:
Code:
PARRDR> WARNING: ATOMS IN BOND OC2D CC2O 700.00000 1.21500 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CC2O CC33 330.00000 1.50000 DONT EXIST
PARRDR> WARNING: ATOMS IN BOND CC2O CC31 330.00000 1.50000 DONT EXIST
containing carbohydrate atom types truncated to 4 characters. However, c35b3 happens to be the version I'm currently using for my routine CGenFF work, and I've never encountered such problems. I happen to have "IOFOrmat EXTEnd" as the first line in all my CGenFF input files, but that shouldn't be the difference.

Originally Posted By: rmv
Then it is more likely that there's an error in the modified files somewhere, like a duplicate name ...
The atom type DUM is defined both in the carbohydrate and in the protein force field. I'd imagine one of them should probably be removed when streaming in both force fields.

Re: About CHARMM General Force Field
Kenno #24209 05/07/10 04:37 PM
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The four letter atom names did make me wonder which version was being used.

Besides DUM, the water atoms are another common conflict when merging RTF/PARAM file pairs.


Rick Venable
computational chemist

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