[gmx-users] Phosphorylated Amino Acids

Graham Smith smithgr at cancer.org.uk
Fri May 10 14:05:03 CEST 2002


Well "a couple of days" has turned into a month but here are my files
for phosphorylated amino acids if anyone wants to use/check/critically
assess them. It sounds like they are about to be overtaken by v 4.0
history anyway. They contain SEP (phosphoserine), TPO
(phosphothreonine), and PTR (phosphotyrosine) (all PO4^{2-} forms),
and SEPH, TPOH, PTRH (PO4H^{-} forms).

The charges and vdw parameters come from Hansson, Nordlund and Aqvist
jmb 265 118-27 1997. They worked with gromos 87 but I generally
use gromos 96 so I've made the files in that format (there seem to be
no differences in the amino acid charges between 87 and 96).  Hansson
et al don't report bond angle or dihedral parameters, and I don't know
how to do QM calculations, so I've used the standard forms from the
*bon.itp file.  For the dihedrals, I've used the 3-fold gd_11.
Because of their symmetry, the PO4^{2-} forms at least cannot have the
2-fold + 3-fold symmetry used in the gmx DNA bases.

I've checked that I can build simple 1-molecule topologies and tprs
for the P04H forms, and for the PO4 forms have done 100 ps solvated MD
of the isolated am acs and the am acs in proteins (1f1w, 1fu0, 1qmz).
I've checked parameters in gmxdumped tprs.

quite a few ff files need modifying, so I provide pamac_hsn.atp
pamac_hsn.hdb pamac_hsnnb.itp pamac_hsn.rtp and makeff.pl
uuencoded tar.gz file thats on the end of the message. 

if you set up the gromacs environment and then run
makeff.pl 
it will get the ffG43a1* files from the top/ directory and make 
local versions called ffG43mod*.
It also makes local modified copies of FF.dat, aminoacids.dat vdwradii.dat

You then have to modify the ffG43modnb.itp file slightly as the extra stuff 
is just added at the end; move the definition of atom type OP to the 
top [ atomtypes ] section. 

There are a few lines at the top of the perlscript you can modify to
change the names.  I think any of the ffG43 versions will work
unmodified; if you use the ffgmx files, then you have to sort out the
includes for ga_nn gb_nn etc manually (or with cpp?).

Then copy the ffG43mod* FF.dat aminoacids.dat vdwradii.dat files back
to the gmx topology directory (having made backups first...)

Graham

########################################################################

Dr. Graham R. Smith, 		       Department of Biological Sciences,  
Biomolecular Modelling Laboratory,     Biochemistry Building,              	
Cancer Research UK, 		       Imperial College of Science,        	
44 Lincoln's Inn Fields, 	        Technology & Medicine,             	
London WC2A 3PX,		       London SW7 2AZ,                     	
U.K. 				       U.K.                                	
Tel: +44-(0)20 7269 3348 	       Tel: +44-(0)20 7594 5734            	
email: graham.smith at cancer.org.uk	
URL: http://www.bmm.icnet.uk/~smithgr

########################################################################

begin 644 pamac_dist.tar.gz
M'XL("(JEVSP``W!A;6%C7V1I<W0N=&%R`.T]:W?:2);]%?V*&L=[QDYL62\$
MC">3=F/'9$]BO$EZ>S<O1T8"U`:)EH0=3R;SV_?>6R6I2 at B2;,=.>P;U:0QU
M'W7KO at N%TO.C@\-G1[H?IMD/-W49IF&XCO.#`6^:)OZ%RS7X7\-P+!O&6H[K
MMBRK:<.X:;8LXP=FW)A$TC5/,R]A[(=T&F;C4;(4[WPZO0UQ;OO2?@DF$[;A
ML4$\GTT"%@^9[UVG&VSLI2R;)U'@LS#*8N:Q:1QE8W8^S]@X2`+FP?_3:S8,
M)T&J#>.$S<9Q"O\GUQ,O`RIO&D9`- at C]E(5#YD77<12P*R_*@'',YFFP-Q@'
M at XN]01)FX<";3*XU+TV#%,#C8*JS)QE+XWD$Y)/P(L#!:YK4.X]!!F!Q#N)>
M!DGF7001.[]FE\S1#6T,K at Q"X(17WK7.7B+=`&3WPHB].#IE6T+0-$C"*-C>
M82]/^UH^F(V3(([XN!?Y[/3E\X(@NT[B%$%L"Z1EIWWGW4=K]Q.#Q4_3[1T-
M\6&"'G&$5Z#ML2U`Z[W[6*#IF at 82L<'82T9!2G-<^E=LYB7>-,B")`59IP$;
M)O&4];PH3>-HAYW$B3\!51#ZP6^7L$3MU^DYL]PF,\WVKM5B9J?3$HN]BI,+
M,,`T3K,)?`*_9B-@%Z>LW2+[/6&C(`H24CG8(8=V7%`X>_+G2S"LYY/&N7G!
M`^"#E]$2X,]61AZ0!L&4VT$#2_OA<`BCT2#'#R07*-9['F17`9 at +),&U=-QM
MG>7KU(*,>1/FQ]&?,Y8$LSC)V'E,JQZA:R8PQSCP06Y)7=Q,3P35111?:>/X
M"L7R8_9?SQ at XUF`.'AG&$>#FZX-5^R0B1'_D>XG/K</5#N/:?9A8#[,9*0!$
M?`RS(WXN`?!2&=F[PWCBLY%_9IJZ]E,P\%"S$$X`#!.67D]!WN1ZAY!5UV&@
MTDG at I1D(&T4QQ)=W2=K7+,[T0<X]Y\*G%5H>33^PPY,#=NY!\(![D5P46B2:
MA_8&QF#Y$%F$4XQS<W<:3P+0#$P4S^))/`J%-V:SA,<S"6HX/2XDUW,QWG>$
M["2KCZ$-69[-4E#QY)(2P+-#C2^?A3`F<@)X at YB&_(,^PCIF29P%892R+7-H
M7NTP<S at WX/6WZ=\A8)0%28$"=+!V?SZ=!5QL6/QO\S`#QFP87+'A4+AO%%`X
M@(=>A]&(>P%.>1F"E\^\J3<X&Z>1[F4SK?PT]L]+6'1.SE!"$_B$RYA"\AD.
M]=E$RWT^RSR0U6?S.<1"[*-H7J*/_BX\2=,@&5['<XB>C,UGW(+@=:B((+H,
MDSB:!E&6ZRABR3S2BEF8%F80T9!]1D!.`3H\=FS/O"^6FCLP6G4/O#4)!B(;
M<EF9-HDA)!CDS11#`N-C`C(2&U#1?5`W1B&H"-$A]Q(Z*2\$O$$\0T<!PSY^
MK/M>ML.#G-(\?L9DEGA^&.('3?M?6"BM at KMT+*Q02 at Z?A6Y1?I9.PM$8LY9'
M58`%'[+$@R"=@RVU,&6_0KEFGH]:]?CZ@\C?!ZX\8)@?#,,HQ&!'$;T,E7$]
M"UC_%"='#`T4PUX3""$I>PN6&"`%VN9E4=JX"TT at W:?Y5$@I/'H6)),4"M<L
M(UMB>.4KBS7(==&(RQ.!KZ:0/I[`IS"ZP**4LZ#EEW8 at HV+FUN91KNU])GP%
M4PFGP6`G2^]PO2(TUVV*"9-J(Z2.,!I,YCYZ!(3LR#N+(%C.\37(!F#::([9
MGVT!D`K$8#9[)&I3A$96371?6'N5L84#GGN#"TWH&H45V>5:\L4M$!CBD!<9
MQ)]#VAB&29KINKZM:<>)-_:FFO:]>Z-_ATO)?C<TQV?Z?VCW+>K_3==T6B[`
M3=H&K/O_6[@8P]S(S*;>Z70<@^TSO'C#"R6;Q1^NH5>$+O9A?QL2Y23&5$[=
M&O.H#V78AW9:;!VM=_)2.IH;FF-U_-L.O<?]O]-L-ELVQ7]K'?^W<NT7.S/J
M',?YCC.2=YQ2I%=VG$S;A^[Z2NFT8.C#;G_W=+=?[M=H6P2`-//S;A=VF]":
M#`+<F^,N+$OYK@;[%=SUT8YC1)U.L>F"Z8#):]K&OX6_L,^FO[A+?\MV:5NU
M:^7;JARUE^/V<N2>P,:-N5F@:YK at K(D&,<6W<)VPXG77T*TV>"V-&`3ML?)U
M`=H]P)>>*:#D\?3>).A/!+46H!9"^\?XMG\@YK5=!<I.6?EJZ)"\)6C?I/'^
MJ:!M*[1]:R747 at 4%>5GYBC/;;0ZU"=IGY2M)74)?<[LJ2B6U06-**BC'26TT
M;HAQ/L*GQ7$WQ^^6$\*XPY3Q!R=BO,,4/J1XA0\?X2J'<;,EQOD(5S/BMXH)
M<$CH&0&V"K"6`>PJX+7P<]`+5%\OQ%'O5WJ]0$S^Y0P&%S+9Y>N5M(?=O6WF
M<_1*L%`9@(O5R-0EV,Z5K`"Z!;558P.N60*W:\#"`P!L=7+F_3IJ.V<NS\V-
MH<S-Z9:"98`PF0*6`:>%:,V*A84YB=2NPJP5,%N%Y7PJ=%:["K,K,&LI[#4+
MI[,DGN$7'_6. at M^=+;B+R%J2\G*G"<\H*55U*RS37T`2U!S<E<T0YM'[6LK4
M7R[C+N=<YYI^&<\UX&Z.9!8NM@#.'<TO,\FBH^4.XY>!4@,^+9`<ML2K"O^A
M<J>)`G7;Y6012FG]F,;_8.6D>VR1S/:"S/;*8N.L+#;.72 at VPB!RL>$&))7(
M^`)S783N3A'*3;8$+&Q,8)%-!,4RL,I6+6'R:+6$*3!K!6Q=PA;T+,R0^^A=
MKW.%3];7N8IO5>M<K9/E=8XV8-]_V\2AQY+6JM#NH5E"02I3J9$]#NWEM"JT
M>V at MH;6)UEI"B]#NT;)YL9+UCI;-ZQ#MLGF;1+ML7NINNZ^6:,.E'I;T7],3
MN"M[`G=E3^"N[`G<E3V!N[+JMU96_=9=J/K"/95Q'!&.B=U`4QVW*N,<LU?@
MYZ6=CPM'4_`M5KBG at D^MU]$"?^+0.UK at ST>X0RGXQ/]H at 3\?6<`7(_W<+D5]
MY",WV^4$'P:3.;_CIF3NPCZ at 5^F]5::;(RGU'%F%?7I'IO2^'(=52K:R)/N4
M[V'%1=+I'I8)B/,4%A9\K$(&X1&"UBKF%1;F^,*&5I%<NM)[07M4\%EW?]_X
M*XAN^16$NEF48YU$JTD.>9V1P()B&5AFVY.8B[ES#Y/R at PR6J65PA;F4153F
M5@'.*U4-\RI869B2<A3F1Y)0HI1)8$5F"5PP+V?M+8K&AY0TI3*O!^?,I5GK
M%B8+U>\M at JU58!50_<*J'%W\PDJ"+7QA)<'6W?ZBZXO\^5.54PZHB1(9J1JA
MA5/(,BWPR!UK$:G&^ZK3U?I at 57"9Q^<$/U(RR!(5'"F90$*2I3E4(EI&DJ0Y
M5")35D$I;#<O4Q6D.[H)*TK#DB\;U0)1<JK+)S4[M2JXLE/;QW\O5=SIZOT1
M]FQ?>ZO+U"W[6W\WF<_;=-KR;E`DM'R]=J>M2+6^$?9MNW,QU"L`YOJ+R7^Q
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MAH:_6JH,:O at OO%FCJ0[2!\A)C>YQ`_)0(Q^P^(`E/A\)I%?Y9XOCO-+H'R$T
MK,K\\-YJ0!)JL--&_YCD6<"J(,'<],T5:[C?6$1EGE[C7RP#5DXXNI$Y/G?^
MGP/!+G[_WVK1^7^VT6JNX_\VKGWU+"1M'T\L8N*:>FG*W_%#`N#-C'[D+UT#
M5_Y@\G_-PQL'^HJ25=X>\`^693;YK4=;;UMV)]@U7/J]_LP+DT(8. at S@Z7\R
M:&-VZ1"D%*7#09C"XV<;]0]X/U5,RZCG-_-Y7+/3M$'(CNZV6W:K"3.UJ at 3]
M9U]+<%I#8.J6VW2M)JU%X/U20^#8MNEV4&^F#A-(Z&)/HJ+;3JOIFL3?<6V5
M_\G+KR5X^K4$S[^6X-77$AQ])4'Q?;%"8!B=IM5FS-(-UU4(\IL/*D'3=6V[
MY2*!"<E');`6"6P+W*'3;J/'@C-SQR@([!J"CMTR3)<(.D;+5&=P%@F:3A/X
M`[ZK-SN.PO]YS0IL<#JC[2)[RW%E]/P. at H)N."!RTT*-VFW5K<5&ND`O+D-^
MSY$/?W[VY<B,O5 at 4!%9F0<2 at BAVP5;N0N_NS^:!&[D[+<@W`;NM&TVZ3X&V!
M;WT5/F./*ZZV0O97)RN9F[K1L8U2B<^.:]'MMF.U'6Y2MR7+?E"';S:-EHN:
M:>D=N\,]IC!23>[!>MEJ at RLU=:O3:2L^<%`3N.#OX`4.NDS3-M2@>EPCCFM;
M5K-C82YLFY8B3K<FD3A.$\*J9:%A[:H\/]7(`Q/8EFDX.($)#EVZPK.CFLSF
M.&W#M3!FF[IIMVPYI/JU%*N2\\E!G<4<4)+MHDY-W;45$W2?[E;<AVS0;+=M
MQ$9M(7:3KZ#;JTNUCMUQ(``8IAVK]/WNTUITJ!30%KFH3[-EMV7Q>[4$AM6Q
M#!.E;^EVJV64'O?B\-F+?LT,[7:KY>"WV.!"IFN6)NLN(6A:3MLTVD2`2;J4
MJ5]/`38`S71,-#*&OI1ZNMVG-7FP5)(-7F$ZDI+JT!W3:5FM#FG),#MMV>E>
M/*E8++_4@/_>7=CWNXJ316]PCM7]OVD:KLG[?_`G\!8\_QM"==W_W\9UCY\/
M.OV`70V;3>8IVQ(GTX:9>B(MG="YS;1[=/HID\ZDO<>/EL6#P/B17L,PF/C*
M.:5TI.BY-[C`@THW)^&YCV3SU!L%?ZGR8]#LA]$@3F9QXF5X-!F=++H91FF0
M9/PX\N)LWTT\]I@?7H:K\,.$L^<'+:-(U:-N-_$LV7OTAXY%%KL*+^?%-(T+
M^)!M;!Z=_/?'XV?_<WCP\N#37A;/-M@^TS@>@,7ANWQ0B`?#Q:::`V"B''<:
M^S2&@V=^D`X2!!6GZPI1\8A8/@>=S<H/P5TX7IW.3MZBE>=SDTJV-QB?PO/]
MLRP^\Z9GB`GS<$%A[2:>H8N6$,>ZPI"5#R79;(?AX<=!-M@!"^%)K5S5)`SI
M"B0*(JY4(+5STO)T6!QV\F'U2&":7M-^/)_C>>$@UM8V2A4.V998=!20<;;9
M1\KB]!+/\!3*)R<[8!,TSAZ7?`.PZ%SP`'D at XF9$ZF9_?7+RMWQL,(ZGLRV$
MP%0EUH,'.<+5&`\?WD(:G+4QFZ=CMB5$W&&;9]LYYB?.<!*#G"!.,;X9SS,P
M*1UB_!`/9SX#USO#S?36AA"UP.5KZ?_\$A;S-XEP<3&S!)R=`2:L&B1^PQT*
M(1!G at 3<8HZ^#NG)1N?`%$0<JDLL<006%&W+63%X=(&VK at FP,8%)T/EKFFTA>
MM9#M$]C78MJ/W&,>LK]R:Y%A[Y-!M$+TX7PR.8LG/EA>X.<FWZ31AS)*H6>"
M_).E>\3YS=[>W@@EO\<&\PP"9RBRR\R#>!"V#JZ(F<*'#Q(?E&T/-(&,.!#B
M+4HQSLZ&=(+S1Z+]1!D!"?,XHI.7H_@*SS#$)Q&@:@J)8<:9EXTY_]V!GD%,
M"5$P!PZ'8 at P/9-;XO!!7T8*D?+"4E,04<L9G>&@ZBO61IX!/A"XR`.)07.T&
M@,&1-TC)C4KX_1A5PK$A!URQ)M5#&VK8L-JH`;]KJ.&BL"Z%^BS?Z'.,<\YY
M9)&E%,8KHD8-CB)R&C`+3TUDAC_]D^UYV6P/E8@^=R[.^??$`>:I>`X!/;%B
M'Q_E@*4SK;+?V`?*41BQ/&]3$N>Z$(&$$U?%C7Z7O#5"X(\!5XM0R05Y9H2*
M):H[:9G#>)IAP00H8+;W at YD<P(3X7F8RF"TRX9D*LDA-QH%JQX^?WV9_@>13
MT`MQZRGRVBIH<L$%#18^3Z!.O6L>T,71Z5"&8WS4!4?0V2]X1OLY/XJ=8G2'
MX;-&Z%$,P.D_JFE#9\=X$'H2ST=CX/$!2RE_MDFQ/C$JIA12Z[HNI?HOS$9E
M6J7 at 89?>9`YK6!"J2+(4+"+`J?JHM8?`(I2R8#K3-S>K*-6R68B09 at G;N at BN
METW?*#+3'N(*]VRD_%/- at F'XTQ[Y#G<0=,W2DS]3FVOJV?OI)1.+X at I[SXN7
ML`H]T$)RD7/^"`EZ+`)6S/F4'EF at D8M3@9-&=?9>T-GU;8[:F.'2`1>?YY#@
MLRI(2=I"T\/#%$]IQF2YQ`#4Z"#P'F\:!QE[<?2<Q_9K>OL6'V:`6QZLE?1X
M`UY_>-+8>_?F-9.21;K'>'E-]]Z\+MZ]Y>]$/A')&;J=A$+YC(O7^+32)BLZ
M._49`W4=GN<MZ_`\K^SP`.O!0Y9"UP\;O%S`K^CXYM$$'T:T]VYS[TNZ/\^K
M[_XJR]E>U at 0*^L\T at 9[W#9K`@@X54MBN0K>!4&FR3\MB:45OF.L$V&!$8'/H
M2+U_'A70+XYAJ`B2!9>0=Q"J at BIV+//*N_T]]H]_H$<_$M6:X38U&XQAS>/`
M\V%^8`,Y(+L6C_DHO`"%6>X#18'[4I_YI*D>L\I;E)5N%[KXG)]4/0%7D.NC
MQA7R1$=V?O3H47G&E^F*G8!H;@D/K"HT!OGOE#^J!,J at B<]BR>+IPNRE'RZ=
MO^)'7^Y#FI;.SQ6EP33W('7BP\J8EXSF]&7%%J_J"-]&CP at SR.F87N,,4F.8
M9OO<C%E"SSU*1KJY0W\L_%HBRL()D at Q#_(T!/MR(GJ.D<F#70:93JM5'^(?A
MX]"P()]-XE&M<7$Y?IB<85-$6X-D'IUYDXD.!&!LTA;PP#R&8C]D/Y[E7H2L
M!_CE at BD&R,O_A)T]89.+"R7P at 7T1L2)"^!X`(3HPVBBZ`$I?P+G<#',RP4LF
>(<-][R^LUM?Z6E_K:WVMK_7UNZ__`S`B0H(`>```
`
end













More information about the gromacs.org_gmx-users mailing list