Re: No parameter for ribose ring, Charmm 27

From: Benjamin Hill (ben.luc.chem_at_gmail.com)
Date: Fri May 27 2016 - 05:51:40 CDT

Yes... but then why does ATP work and not my molecule? Here, both have same
atom types.

I would not have to upgrade to charmm36 to run a simulation with ATP... so
why with ITP? No difference in ribose ring atom names or types.

Please help!!
Thank you!!

On May 26, 2016 6:42 PM, "JC Gumbart" <gumbart_at_physics.gatech.edu> wrote:

> 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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