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error while creating psf for a small molecule
#34186 07/17/14 04:14 AM
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vibhor Offline OP
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Hello all :

I have use parachem web server to generate parameters for the small molecule .I was going to generate the psf for the small molecule.I used
top_all36_cgenff.rtf
par_all36_cgenff.prm .
SO while processing it gave error of maximum limit reached .This is my small script :
! get nucleotide definitions and parameters
read rtf card name top_all36_cgenff.rtf
read para card name par_all36_cgenff.prm
stream qnb_para.str



open unit 1 read form name qnb.pdb
read sequence pdb unit 1
close unit 1

! set bomlev to -1 to avoid saying on lack of hydrogen coordinates
bomlev -2
open unit 1 card read name qnb.pdb
read coor pdb unit 1
close unit 1
bomlev 0

! check to see if we have it all (except the hydrogens)
print coor select .not. hydrogen .and. .not. initialized end
ic fill
ic param ! fill in some missing bond and angle information from parameter file
ic build ! try to place missing atoms
! add hydrogens, if needed
hbuild select hydrogen end


! save psf and coordinates
write psf card name qnb.psf

write coor card name qnb.crd








CHARMM> read rtf card name top_all36_cgenff.rtf
VOPEN> Attempting to open::top_all36_cgenff.rtf::
MAINIO> Residue topology file being read from unit 90.
TITLE> * -------------------------------------------------------------------------- *
TITLE> * CGENFF: TOPOLOGY FOR THE CHARMM GENERAL FORCE FIELD V. 2B8 *
TITLE> * FOR SMALL MOLECULE DRUG DESIGN *
TITLE> * -------------------------------------------------------------------------- *
TITLE> *
IN USE MAXIMUM
ATOMS 10007 10000
BONDS 9499 10000
ANGLES 0 10000
DIHEDRALS 0 10000
IMPROPERS 328 4000
CROSSTERMS 0 2000
EXCLUSIONS 0 5000
ACCEPTORS 170 600
DONORS 86 600
BUILD/IC 8734 10000

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

Please help.


Thanks

Re: error while creating psf for a small molecule
vibhor #34189 07/17/14 02:26 PM
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For modern versions of CHARMM (c36b1 and later), you can increase the atom limits at run time; for older versions, you need to recompile with a size keyword that specifies a larger atom limit.

It should be noted that 10,000 atoms has not been one of the standard sizes; on most modern Linux systems, we typically use the XXLARGE size, with a maximum of 360,000 atoms.


Rick Venable
computational chemist

Re: error while creating psf for a small molecule
vibhor #34190 07/17/14 03:03 PM
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Please disregard my initial reply; I misinterpreted the error, it's not related to the number of atoms.

You are missing a GENErate statement, which typically follows the use of READ SEQUence.


Rick Venable
computational chemist

Re: error while creating psf for a small molecule
vibhor #34191 07/17/14 03:21 PM
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Yeah, it's the rtf arrays that are overflowing, not the psf ones. As the "CHARMM size" only influences the latter, changing it won't help.

What vibhor should have done is look at the FAQ before posting. Also, the exact same question has been asked and answered countless times on these forums; here are just 3 of the occurrences returned to me by the forum's search function (note that the recurrence of this question despite its presence in the FAQ had already exceeded my annoyance threshold as far back as 2010):What is the use of a public forum if people don't make use of its accumulated knowledge?! Heck, even just copy-pasting the error message into Google takes you straight to the right answer, in a fraction of the time it takes to get the same answer through the forums, and without wasting any experts' time. Also see the forum guidelines.

Last edited by Kenno; 07/17/14 04:38 PM. Reason: added 3 examples of previous occurrences; rephrased first sentence taking into account Rick's correction.
Re: error while creating psf for a small molecule
vibhor #34192 07/17/14 03:38 PM
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vibhor Offline OP
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Thanks Kenno .

Intent was not to waste experts time.I tried searching for the error. but wasn't able to retrieve.Thanks was directing me to write forums where you answered the concerns before.I will look into that. Thanks !

Re: error while creating psf for a small molecule
vibhor #34193 07/17/14 03:48 PM
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I should probably finish my morning coffee before answering questions in the forum. ;^)

People asking questions should consider doing their homework first, and including the CHARMM version being used in posts.

A GENErate statement will eventually be needed, but is not the cause of the error message posted.


Rick Venable
computational chemist

Re: error while creating psf for a small molecule
vibhor #34195 07/17/14 04:06 PM
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@Rick: sorry, my rant was not aimed at you.
@Vibhor: in your defense, the forum's search function can be considered inoperative for practical purposes. On this occasion, I put in a request to redirect it to our Google search page. If this can be accomplished, it would probably reduce the level of needless friction on this site. wink


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