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AMBER Archive (2003)
Subject: terminal phosphate group in RNA
From: David A. Case (case_at_scripps.edu)
Date: Fri Jan 24 2003 - 18:03:06 CST
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On Thu, Jan 16, 2003, Mahadevan Seetharaman wrote:
>
> Can someone give me suggestions for treating a terminal phosphate group in
> a RNA molecule.
>
> I want a net charge of -1 and I am not sure about the individual charges
> and atom types on the phosphorous and the oxygen atoms... any reference
> on this issue would also be greatly appreciated.
>
This is not as easy as it should be. You basically have to create a terminal
phosphate-capped nucleotide, and link it in.
I'v attached some files we have used for a 5' guanine with an terminal
phosphate, for RNA simulations. The appropriate commands in leap would be:
loadAmberPrep 5gp.prepi
source leaprc.rna.ff99
loadAmberParams frcmod.5gp
x = loadpdb 5gp_test.pdb
saveAmberParm x prmtop prmcrd
Notes:
With just an obvious phosphate force field, bad things can happen with the
terminal H atom. We "cheated" by adding an artificial P--H bond to keep the
geometry of the terminal P-O-H group fixed (as in TIP3P water, for example).
Because of the above, you have to load this prep file *before* loading the
leaprc file. This is a bug in leap, which will get fixed, but for now, this
workaround should do. (Try the other order to see the problem.)
Charges above are RESP for this nucleotide; you would need to do something
similar for the A,C,U if you needed those...
.hope this helps...good luck...dac
[Note: I forgot that the reflector won't take attachments....files are
added below as text instead....]
--================================================================== David A. Case | e-mail: case_at_scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | http://www.scripps.edu/case ==================================================================
====================== 5gp.prepi========================================== 0 0 0
5' guanine with capped phosphate 5GP.res 5GP INT 0 CHANGE NOMIT DU BEG 0.00000 1 DUMM DU M 0.000000 0.000000 0.000000 0.0 2 DUMM DU M 1.000000 0.000000 0.000000 0.0 3 DUMM DU M 1.000000 1.000000 0.000000 0.0 4 H5T HO M 1.404339 0.042249 0.165634 0.396800 5 O3P OH E 1.114476 0.908491 -0.241311 -0.721900 6 P P M 2.314489 1.776673 -0.478436 1.320100 7 O1P O2 E 1.933410 3.073374 -1.081549 -0.816600 8 O2P O2 E 3.156547 0.871841 -1.292450 -0.816600 9 O5' OS M 2.994369 2.142475 0.922974 -0.558300 10 C5' CT M 2.156035 2.551837 2.019887 0.055800 11 H5'1 H1 E 1.452687 1.753841 2.257803 0.067900 12 H5'2 H1 E 1.604968 3.450028 1.741178 0.067900 13 C4' CT M 3.008252 2.847921 3.243186 0.106500 14 H4' H1 E 2.447118 3.477373 3.933851 0.117400 15 O4' OS S 3.228121 1.605168 3.977231 -0.354800 16 C1' CT 3 4.558614 1.150950 3.777548 0.019100 17 H1' H2 E 5.072002 1.095281 4.737461 0.200600 18 C2' CT B 5.230443 2.095696 2.779425 0.067000 19 H2'1 H1 E 5.668211 2.081313 1.781301 0.097200 20 O2' OH S 6.272982 2.049941 3.757136 -0.613900 21 HO'2 HO E 6.759278 1.235228 3.610987 0.418600 22 N9 N* B 4.499533 -0.267934 3.326576 0.049200 23 C4 CB B 4.673998 -1.376548 4.117501 0.122200 24 C5 CB B 4.535095 -2.474583 3.310330 0.174400 25 C6 C B 4.665031 -3.772051 3.872552 0.477000 26 O6 O E 4.578059 -4.865457 3.315956 -0.559700 27 N1 NA B 4.925924 -3.709096 5.246587 -0.478700 28 H1 H E 5.032526 -4.575560 5.734311 0.342400 29 C2 CA S 5.047712 -2.547461 5.981551 0.765700 30 N2 N2 B 5.299265 -2.702442 7.288571 -0.967200 31 H21 H E 5.396738 -3.573950 7.789643 0.436400 32 H22 H E 5.381214 -1.857324 7.835527 0.436400 33 N7 NB E 4.278741 -2.081203 2.002035 -0.570900 34 N3 NC E 4.927829 -1.332945 5.452892 -0.632300 35 C8 CK S 4.267504 -0.772686 2.063331 0.137400 36 H8 H5 E 4.096308 -0.099877 1.236033 0.164000 37 C3' CT M 4.415606 3.377827 2.961306 0.202200 38 H3' H1 E 4.412072 3.941489 2.028369 0.061500 39 O3' OS M 5.029898 4.128649 3.998279 -0.524600
LOOP O3P P C2' C3' C2 N3 C8 N7
IMPROPER C4 C8 N9 C1' H8 N9 C8 N7 C6 C4 C5 N7 C5 N1 C6 O6 C6 C2 N1 H1 N2 N1 C2 N3 C2 H21 N2 H22 C5 N9 C4 N3 -M O3P H5T P
DONE STOP
================== frcmod.5gp ============================================ # parameters for 5' guanine with phospphate group
BOND P - HO 300.0 2.1200
ANGLE P - HO - OH 0.0 0.00 O2 - P - HO 0.0 0.00 OS - P - HO 0.0 0.00 OH - P - HO 0.0 0.00 DIHE OS-P-HO-OH 2 0.00 0 2.0 O2-P-HO-OH 2 0.00 0 2.0
==================== 5gp_test.pdb=========================================== ATOM 1 P 5GP A 1 -11.508 -25.691 -0.634 1.00 0.00 P ATOM 2 O1P 5GP A 1 -10.812 -25.657 -1.940 1.00 0.00 O ATOM 3 O2P 5GP A 1 -12.742 -24.897 -0.437 1.00 0.00 O ATOM 4 O5* 5GP A 1 -10.453 -25.271 0.508 1.00 0.00 O ATOM 5 C5* 5GP A 1 -9.926 -23.963 0.550 1.00 0.00 C ATOM 6 C4* 5GP A 1 -8.954 -23.845 1.721 1.00 0.00 C ATOM 7 O4* 5GP A 1 -7.803 -24.643 1.522 1.00 0.00 O ATOM 8 C3* 5GP A 1 -8.414 -22.431 1.869 1.00 0.00 C ATOM 9 O3* 5GP A 1 -9.347 -21.558 2.467 1.00 0.00 O ATOM 10 C2* 5GP A 1 -7.199 -22.695 2.739 1.00 0.00 C ATOM 11 O2* 5GP A 1 -7.527 -22.689 4.110 1.00 0.00 O ATOM 12 C1* 5GP A 1 -6.755 -24.092 2.307 1.00 0.00 C ATOM 13 N9 5GP A 1 -5.506 -24.023 1.526 1.00 0.00 N ATOM 14 C8 5GP A 1 -5.344 -23.903 0.170 1.00 0.00 C ATOM 15 N7 5GP A 1 -4.097 -23.877 -0.212 1.00 0.00 N ATOM 16 C5 5GP A 1 -3.380 -23.986 0.976 1.00 0.00 C ATOM 17 C6 5GP A 1 -1.977 -24.014 1.190 1.00 0.00 C ATOM 18 O6 5GP A 1 -1.075 -23.949 0.356 1.00 0.00 O ATOM 19 N1 5GP A 1 -1.671 -24.132 2.538 1.00 0.00 N ATOM 20 C2 5GP A 1 -2.598 -24.216 3.557 1.00 0.00 C ATOM 21 N2 5GP A 1 -2.114 -24.323 4.802 1.00 0.00 N ATOM 22 N3 5GP A 1 -3.919 -24.192 3.356 1.00 0.00 N ATOM 23 C4 5GP A 1 -4.235 -24.075 2.045 1.00 0.00 C ATOM 35 P RG A 2 -9.009 -19.995 2.665 1.00 0.00 P ATOM 36 O1P RG A 2 -10.162 -19.355 3.337 1.00 0.00 O ATOM 37 O2P RG A 2 -8.523 -19.464 1.373 1.00 0.00 O ATOM 38 O5* RG A 2 -7.773 -20.012 3.697 1.00 0.00 O ATOM 39 C5* RG A 2 -7.955 -20.395 5.043 1.00 0.00 C ATOM 40 C4* RG A 2 -6.619 -20.349 5.783 1.00 0.00 C ATOM 41 O4* RG A 2 -5.656 -21.151 5.126 1.00 0.00 O ATOM 42 C3* RG A 2 -6.019 -18.949 5.825 1.00 0.00 C ATOM 43 O3* RG A 2 -6.615 -18.142 6.818 1.00 0.00 O ATOM 44 C2* RG A 2 -4.568 -19.283 6.118 1.00 0.00 C ATOM 45 O2* RG A 2 -4.334 -19.420 7.501 1.00 0.00 O ATOM 46 C1* RG A 2 -4.369 -20.620 5.410 1.00 0.00 C ATOM 47 N9 RG A 2 -3.612 -20.434 4.158 1.00 0.00 N ATOM 48 C8 RG A 2 -4.086 -20.202 2.893 1.00 0.00 C ATOM 49 N7 RG A 2 -3.152 -20.087 1.992 1.00 0.00 N ATOM 50 C5 RG A 2 -1.972 -20.255 2.710 1.00 0.00 C ATOM 51 C6 RG A 2 -0.625 -20.235 2.259 1.00 0.00 C ATOM 52 O6 RG A 2 -0.205 -20.062 1.116 1.00 0.00 O ATOM 53 N1 RG A 2 0.263 -20.444 3.304 1.00 0.00 N ATOM 54 C2 RG A 2 -0.095 -20.650 4.621 1.00 0.00 C ATOM 55 N2 RG A 2 0.905 -20.836 5.493 1.00 0.00 N ATOM 56 N3 RG A 2 -1.364 -20.671 5.045 1.00 0.00 N ATOM 57 C4 RG A 2 -2.243 -20.467 4.037 1.00 0.00 C
- Next message: Seongeun Yang: "Re: problems in equilibrating NaCl solution"
- Previous message: David A. Case: "Re: problems in equilibrating NaCl solution"
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