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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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