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5TER patch on RNA
#37840 04/17/20 09:36 AM
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Nadia Offline OP
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Hi Lennart,

I am trying to generate a strand of RNA (six URA) using the 5TER patch included in top_all36_na.rtf
I am getting a non-integer charge after using the following gene command:
CHARMM> read sequ ura 6
CHARMM> gene rnaa setup first 5ter last none warn

THE PATCH '5TER' WILL BE USED FOR THE FIRST RESIDUE
NO PATCHING WILL BE DONE ON THE LAST RESIDUE
** WARNING ** BOND NOT FOUND FOR RESIDUE 1 URA .
ATOMS "P " "O1P " WERE REQUESTED.
** WARNING ** BOND NOT FOUND FOR RESIDUE 1 URA .
ATOMS "P " "O2P " WERE REQUESTED.
** WARNING ** BOND NOT FOUND FOR RESIDUE 1 URA .
ATOMS "P " "O5' " WERE REQUESTED.
** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 URA .
ATOMS "O1P " "P " WERE REQUESTED.
** WARNING ** ACCEPTOR NOT FOUND FOR RESIDUE 1 URA .
ATOMS "O2P " "P " WERE REQUESTED.
** WARNING ** BOND NOT FOUND FOR RESIDUE 6 URA .
ATOMS "O3' " "+P " WERE REQUESTED.
GENPSF> Segment 1 has been generated. Its identifier is RNAA.

Warning from PSFSUM: The sum of charges ( -5.470000) is not an integer

I see that the patch removes O=P=O while building the terminus, and
I am capable of adjusting the charges, but shouldn't the patch
do those things? What am I missing?

Re: 5TER patch on RNA
Nadia #37841 04/17/20 01:39 PM
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Your problem is with the 3'-terminal residue. You have asked that no patch should be applied to the 3'-terminal ("last none"), and this is probably not what you want. It leaves you wtih a 3'-terminal residue trying to link to a non-existent following residue. The warnings regarding the 5'-terminal residue can safely be ignored since the refer to atoms that have been actively deleted by the 5ter patch, in contrast to atom "+P" which is expected at the non-patched 3'-terminal. You can remove the WARN keyword to avoid having all these warnings listed.

Last edited by lennart; 04/17/20 01:52 PM.

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: 5TER patch on RNA
lennart #37843 04/17/20 04:59 PM
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Nadia Offline OP
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That was exactly the problem. Thank you so much.


Moderated by  John Legato, lennart 

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