Re: No parameter for ribose ring, Charmm 27

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Thu May 26 2016 - 18:42:52 CDT

C2’ is type CN7B in CHARMM36. You should update your model using the latest force field anyway, which will probably also solve your issue.

Best,
JC

> On May 26, 2016, at 6:18 PM, Benjamin Hill <ben.luc.chem_at_gmail.com> wrote:
>
> Hello,
> I am trying to make topology file for inosine triphosphate (ITP). ITP has a very similar structure to ATP. Long story short... I used ATP as a structural template. I remove the adenine "group" and attach the new "group" to create ITP... and prepared the new ITP topology file (again, using ATP as a template -- I removed the adenine group and attached the new one to make ITP).
> When I run the simulation, I get a weird error -- it says it' can't identify certain parameters for parts of the ribose ring of ITP -- even though I did not touch this section of the ATP template in order to create the ITP. For instance, it says it' can't angle parameters for atoms C4' - C3' - C2' which are atom types CN7-CN7-CN7. Indeed it is true -- there are no such parameters in the parameter file for this angle. But this is for ribose. When I run ATP simulation it is fine, but not for ITP.
> What is going on?
>
> Here is my ITP topology file (residue name is ITX)
> -- Below it is a copy of a PDB for an ITP molecule
>
>
> RESI ITX -4.00 !
> !
> !
> GROUP !
> ATOM C4' CN7 0.16 !
> ATOM H4' HN7 0.09 !
> ATOM O4' ON6B -0.50 ! O6 (N6, H61, H62 removed)
> ATOM C1' CN7B 0.16 ! ||
> ATOM H1' HN7 0.09 ! NEW for ITP-> H1 C6
> GROUP ! \ / \
> ATOM C5 CN5G 0.00 ! N1 C5--N7\\
> ATOM N7 NN4 -0.60 ! | || C8-H8
> ATOM C8 CN4 0.25 ! C2 C4--N9/
> ATOM H8 HN3 0.16 ! / \\ / \
> ! H2 N3 \
> ! \
> ATOM N1 NN2G -0.32 ! \
> ATOM H1 HN2 0.26 !!!! NEW FOR ITP |
> ATOM N9 NN2B -0.01 ! |
> ! |
> ! |
> ATOM O6 ON1 -0.51 ! \
> ATOM C2 CN4 0.50 ! \
> ATOM H2 HN3 0.08 ! (-)O3G O2B O1A H5' H4' O4' \
> ATOM N3 NN3I -0.61 ! | | | | \ / \ |
> ATOM C4 CN5 0.26 !O1G=PG-O3B-PB-O3A-PA-O5'-C5'---C4' C1'
> ATOM C6 CN1 0.54 ! | | | | \ / \
> ! (-)O2G (-)O1B (-)O2A H5'' C3'--C2' H1'
> ! / \ / \
> ! O3' H3' O2' H2''
> ! | |
> ! H3T H2'
> !
> !
> GROUP !
> ATOM C2' CN7 0.14 !
> ATOM H2'' HN7 0.09
> ATOM O2' ON5 -0.66
> ATOM H2' HN5 0.43
> GROUP
> ATOM C3' CN7 0.14
> ATOM H3' HN7 0.09
> ATOM O3' ON5 -0.66
> ATOM H3T HN5 0.43
> GROUP
> ATOM C5' CN8 -0.08
> ATOM H5' HN8 0.09
> ATOM H5'' HN8 0.09
> ATOM O5' ON2 -0.62
> ATOM PA P 1.50
> ATOM O1A ON3 -0.82
> ATOM O2A ON3 -0.82
> ATOM O3A ON2 -0.74
> ATOM PB P2 1.50
> ATOM O1B ON3 -0.82
> ATOM O2B ON3 -0.82
> ATOM O3B ON2 -0.86
> ATOM PG P2 1.10
> ATOM O1G ON3 -0.90
> ATOM O2G ON3 -0.90
> ATOM O3G ON3 -0.90
>
> BOND C6 N1
> BOND O5' C5' O5' PA PA O1A PA O2A PA O3A
> BOND O3A PB PB O1B PB O2B PB O3B O3B PG
> BOND PG O1G PG O2G PG O3G
> BOND C5' C4' C4' O4' C4' C3' O4' C1'
> BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3
> BOND C2 N1
> BOND N1 H1
> BOND C6 C5 C5 N7
> BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' H3T
> BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
> BOND C5' H5'' C8 H8 C2 H2
> DOUBLE C6 O6
> DOUBLE N3 C2
> DOUBLE C4 C5
> DOUBLE N7 C8
> IMPR C6 N1 C5 O6
> IMPR C2 N1 N3 H2
>
> PATC FIRS NONE LAST NONE
>
>
>
>
> ############
> HERE IS THE ITP PDB:
> ############
>
> ATOM 1 PA ITX A 426 57.691 -8.399 58.192 1.00 0.00 ITX P
> ATOM 2 PB ITX A 426 59.580 -6.656 58.876 1.00 0.00 ITX P
> ATOM 3 PG ITX A 426 60.579 -6.580 56.252 1.00 0.00 ITX P
> ATOM 4 C5' ITX A 426 56.437 -10.527 59.062 1.00 0.00 ITX C
> ATOM 5 O5' ITX A 426 57.089 -9.297 59.376 1.00 0.00 ITX O
> ATOM 6 C4' ITX A 426 55.091 -10.635 59.927 1.00 0.00 ITX C
> ATOM 7 O4' ITX A 426 55.321 -10.831 61.277 1.00 0.00 ITX O
> ATOM 8 C3' ITX A 426 54.086 -9.466 59.815 1.00 0.00 ITX C
> ATOM 9 O3' ITX A 426 52.715 -9.964 59.922 1.00 0.00 ITX O
> ATOM 10 C2' ITX A 426 54.537 -8.666 61.056 1.00 0.00 ITX C
> ATOM 11 O2' ITX A 426 53.508 -7.808 61.601 1.00 0.00 ITX O
> ATOM 12 C1' ITX A 426 54.925 -9.710 62.048 1.00 0.00 ITX C
> ATOM 13 N1 ITX A 426 55.869 -8.550 66.999 1.00 0.00 ITX N1
> ATOM 14 O1A ITX A 426 58.788 -9.190 57.584 1.00 0.00 ITX O
> ATOM 15 O1B ITX A 426 59.543 -5.585 59.959 1.00 0.00 ITX O
> ATOM 16 O1G ITX A 426 61.649 -5.564 56.369 1.00 0.00 ITX O
> ATOM 17 O6 ITX A 426 58.050 -8.264 66.990 1.00 0.00 ITX O
> ATOM 18 C2 ITX A 426 54.727 -8.711 66.355 1.00 0.00 ITX C
> ATOM 19 O2A ITX A 426 56.645 -7.978 57.217 1.00 0.00 ITX O
> ATOM 20 O2B ITX A 426 60.459 -7.891 59.050 1.00 0.00 ITX O
> ATOM 21 O2G ITX A 426 60.884 -8.050 56.516 1.00 0.00 ITX O
> ATOM 22 N3 ITX A 426 54.536 -9.112 65.115 1.00 0.00 ITX N
> ATOM 23 O3A ITX A 426 58.048 -7.150 58.981 1.00 0.00 ITX O
> ATOM 24 O3B ITX A 426 59.553 -6.040 57.378 1.00 0.00 ITX O
> ATOM 25 O3G ITX A 426 59.755 -6.560 54.929 1.00 0.00 ITX O
> ATOM 26 C4 ITX A 426 55.744 -9.158 64.424 1.00 0.00 ITX C
> ATOM 27 C5 ITX A 426 56.989 -9.002 64.967 1.00 0.00 ITX C
> ATOM 28 C6 ITX A 426 57.063 -8.657 66.351 1.00 0.00 ITX C
> ATOM 29 N7 ITX A 426 57.989 -9.178 63.962 1.00 0.00 ITX N
> ATOM 30 C8 ITX A 426 57.265 -9.373 62.852 1.00 0.00 ITX C
> ATOM 31 N9 ITX A 426 55.929 -9.362 63.062 1.00 0.00 ITX N
> ATOM 32 H1 ITX A 426 56.001 -8.211 68.403 1.00 0.00 ITX H
> ATOM 34 H2 ITX A 426 53.836 -8.527 66.954 1.00 0.00 ITX H
> ATOM 35 H8 ITX A 426 57.736 -9.480 61.874 1.00 0.00 ITX H
> ATOM 36 H1' ITX A 426 54.065 -10.145 62.601 1.00 0.00 ITX H
> ATOM 37 H2' ITX A 426 52.720 -8.343 61.724 1.00 0.00 ITX H
> ATOM 38 H3' ITX A 426 54.104 -8.758 58.959 1.00 0.00 ITX H
> ATOM 39 H4' ITX A 426 54.622 -11.596 59.627 1.00 0.00 ITX H
> ATOM 40 H5' ITX A 426 57.007 -11.421 59.392 1.00 0.00 ITX H
> ATOM 41 H3T ITX A 426 52.809 -10.870 59.617 1.00 0.00 ITX H
> ATOM 42 H2'' ITX A 426 55.477 -8.130 60.805 1.00 0.00 ITX H
> ATOM 43 H5'' ITX A 426 56.271 -10.685 57.975 1.00 0.00 ITX H
> END

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