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popc error
#28466 10/17/11 05:17 PM
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prakash Offline OP
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I have the follwing input and out for generating POPC membrane patch. I found a follwing error,

RESIDUE SEQUENCE -- 475 RESIDUES
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC
POPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPCPOPC

CHARMM> generate HETA setup warn first none last none
NO PATCHING WILL BE DONE ON THE FIRST RESIDUE
NO PATCHING WILL BE DONE ON THE LAST RESIDUE
<CODES>: No angle parameters for 1 ( NTL CTL5 NTL )
<CODES>: No angle parameters for 2 ( NTL CTL5 NTL )
<CODES>: No angle parameters for 3 ( NTL CTL5 NTL )
<CODES>: No angle parameters for 4 ( NTL CTL5 NTL )
<CODES>: No angle parameters for 5 ( CTL2 CTL5 NTL )
<CODES>: No angle parameters for 6 ( CTL2 CTL5 NTL )
<CODES>: No angle parameters for 9 ( CTL2 CTL5 NTL )
<CODES>: No angle parameters for 10 ( CTL2 CTL5 NTL )
<CODES>: No angle parameters for 11 ( CTL2 CTL5 CTL2)
<CODES>: No angle parameters for 12 ( CTL2 CTL5 CTL2)
<CODES>: No angle parameters for 13 ( CTL2 CTL5 CTL2)
<CODES>: No angle parameters for 14 ( CTL2 CTL5 CTL2)
<CODES>: No angle parameters for 15 ( CTL2 CTL5 CTL2)
<CODES>: No angle parameters for 16 ( CTL2 CTL5 CTL2)
<CODES>: No angle parameters for 19 ( CTL5 CTL5 CTL5)
<CODES>: No angle parameters for 20 ( CTL5 CTL5 CTL5)
<CODES>: No angle parameters for 21 ( NTL CTL5 CTL5)
<CODES>: No angle parameters for 22 ( NTL CTL5 CTL5)
<CODES>: No angle parameters for 23 ( NTL CTL5 CTL5)
<CODES>: No angle parameters for 24 ( NTL CTL5 CTL5)
<CODES>: No angle parameters for 25 ( NTL CTL5 CTL5)
<CODES>: No angle parameters for 26 ( NTL CTL5 CTL5)
<CODES>: No angle parameters for 27 ( NTL CTL5 CTL5)
<CODES>: No angle parameters for 28 ( NTL CTL5 CTL5)
<CODES>: No angle parameters for 29 ( NTL CTL5 CTL5)
<CODES>: And more missing angle parameters.
<CODES>: A TOTAL OF 7935 MISSING PARAMETERS

***** LEVEL -1 WARNING FROM <CODES> *****
***** CODES> MISSING PARAMETERS
******************************************
BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 5


***** LEVEL -2 WARNING FROM <AUTGEN> *****
***** DOUBLE BOND SPECS FOR SOME ATOM PAIRS
******************************************
BOMLEV ( -2) IS REACHED - TERMINATING. WRNLEV IS 5
Could you let me know how to solve this issue. I am using c35b1.

Attached Files
che.txt (51.58 KB, 268 downloads)
Last edited by prakash; 10/17/11 05:19 PM.
Re: popc error
prakash #28467 10/17/11 06:15 PM
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rmv Online Content
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Clearly a bug of some kind, as those angle terms should not exist in any PC lipids. The PSF building process has been derailed in some way, possibly by reading the sequence from the PDB file. The long list of 'SEQRDR> Residue insertion' messages may indicate a format issue with the PDB file. Try replacing

READ SEQU PDB UNIT 10

with

READ SEQU POPC 475


Rick Venable
computational chemist

Re: popc error
rmv #28468 10/17/11 06:43 PM
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prakash Offline OP
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Charmm-gui solved this issue, but when I run classical charmm run with READ SEQU POPC 475, again It shows the follwing error
CODES>: A TOTAL OF 7935 MISSING PARAMETERS

***** LEVEL -1 WARNING FROM <CODES> *****
***** CODES> MISSING PARAMETERS
******************************************
BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 5


***** LEVEL -2 WARNING FROM <AUTGEN> *****
***** DOUBLE BOND SPECS FOR SOME ATOM PAIRS
******************************************
BOMLEV ( -2) IS REACHED - TERMINATING. WRNLEV IS 5

Re: popc error
prakash #28469 10/17/11 07:29 PM
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The standard approach, given the information you have (CHARMM GUI works,"CLASSICAL" CHARMM results in error), towards resolving the issue is to check the differences between the two protocols. I do not understand why you did not do this.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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