AMBER Archive (2006)
Subject: Re: AMBER: Problem with specifying NOSHAKEMASK

From: Gobind Singh Bisht (gsbisht1_at_gmail.com)
Date: Sun Dec 03 2006 - 09:26:27 CST

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hi carlos,
i'm using amber9 on cygwin.I have run the test suite and got only
these errors which doesnt seems to be related to mask specification.:
-----------------------------------------------------------------------------------------------------------------
possible FAILURE: check mdout.jar.dif
/home/Debabrata/amber9/test/jar
187c187
< Etot = -3528.1878 EKtot = 514.2873 EPtot = -
4042.4750

--- > Etot = -3528.1877 EKtot = 514.2873 EPtot = - 4042.4750 --------------------------------------- possible FAILURE: check nma.out.dif /home/Debabrata/amber9/test/qmmm2/pure_QM_MD_PDDGPM3 137c137 < 7 -4.998E+1 3.451 1.202E+1 O 6 --- > 7 -4.998E+1 3.451 1.203E+1 O 6 143c143 < 8 -5.012E+1 5.273 2.036E+1 O 6 --- > 8 -5.012E+1 5.274 2.036E+1 O 6 149c149 < 9 -4.757E+1 2.643E+1 1.099E+2 C 5 --- > 9 -4.757E+1 2.642E+1 1.099E+2 C 5 153c153 < PDDGPM3-ESCF= -47.577 --- > PDDGPM3-ESCF= -47.578 --------------------------------------- possible FAILURE: check crambin_md_calc_mulliken.out.dif /home/Debabrata/amber9/test/qmmm2/crambin_2 199c199 < Etot = -1019.2203 EKtot = 17.4915 EPtot = - 1036.7117 --- > Etot = -1019.2203 EKtot = 17.4914 EPtot = - 1036.7117 --------------------------------------- possible FAILURE: check amoeba_jac.mdout.dif /home/Debabrata/amber9/test/amoeba_jac 206c206 < EKCMT = 0. VIRIAL = 0. VOLUME = 0.0013 --- > EKCMT = 0. VIRIAL = 0. VOLUME = 0.0028 --------------------------------------- possible FAILURE: check ash.mol2.dif /home/Debabrata/amber9/test/antechamber/ash 9c9 < 3 HH32 1.486 2.454 0.890 hc 1 ACE 0.066 --- > 3 HH32 1.486 2.454 0.890 hc 1 ACE 0.065 12,18c12,18 < 6 O 4.391 1.877 0. o 1 ACE 0.606 < 7 N 3.555 3.970 0. n 1 ASH 0.575 < 8 H 2.733 4.556 0. hn 1 ASH 0.334 < 9 CA 4.853 4.614 0. c3 1 ASH 0.047 < 10 HA 5.408 4.316 0.890 h1 1 ASH 0.111 < 11 CB 5.661 4.221 1.232 c3 1 ASH 0.150 < 12 HB2 5.809 3.141 1.241 hc 1 ASH 0.105 --- > 6 O 4.391 1.877 0. o 1 ACE 0.608 > 7 N 3.555 3.970 0. n 1 ASH 0.576 > 8 H 2.733 4.556 0. hn 1 ASH 0.336 > 9 CA 4.853 4.614 0. c3 1 ASH 0.050 > 10 HA 5.408 4.316 0.890 h1 1 ASH 0.107 > 11 CB 5.661 4.221 1.232 c3 1 ASH 0.152 > 12 HB2 5.809 3.141 1.241 hc 1 ASH 0.107 24,31c24,31 < 18 C2 4.713 6.129 0. c 1 ASH 0.639 < 19 O1 3.601 6.653 0. o 1 ASH 0.625 < 20 N1 5.846 6.835 0. n 1 NME 0.559 < 21 H4 6.737 6.359 0. hn 1 NME 0.340 < 22 C1 5.846 8.284 0. c3 1 NME 0.076 < 23 H1 4.819 8.648 0. h1 1 NME 0.074 < 24 H2 6.360 8.648 0.890 h1 1 NME 0.035 < 25 H3 6.360 8.648 0.890 h1 1 NME 0.030 --- > 18 C2 4.713 6.129 0. c 1 ASH 0.640 > 19 O1 3.601 6.653 0. o 1 ASH 0.623 > 20 N1 5.846 6.835 0. n 1 NME 0.560 > 21 H4 6.737 6.359 0. hn 1 NME 0.339 > 22 C1 5.846 8.284 0. c3 1 NME 0.077 > 23 H1 4.819 8.648 0. h1 1 NME 0.073 > 24 H2 6.360 8.648 0.890 h1 1 NME 0.037 > 25 H3 6.360 8.648 0.890 h1 1 NME 0.029 --------------------------------------- possible FAILURE: check sustiva.mol2.dif /home/Debabrata/amber9/test/antechamber/sustiva 7c7 < 1 C1 0.728 1.403 0.255 ca 1 SUS 0.049 --- > 1 C1 0.728 1.403 0.255 ca 1 SUS 0.050 10,11c10,11 < 4 C3 0.290 0.932 0.158 c3 1 SUS 0.315 < 5 C4 1.635 0.352 0.032 c1 1 SUS 0.196 --- > 4 C3 0.290 0.932 0.158 c3 1 SUS 0.314 > 5 C4 1.635 0.352 0.032 c1 1 SUS 0.197 21,23c21,23 < 15 C9 0.117 1.500 1.582 c3 1 SUS 0.619 < 16 F1 1.056 2.097 1.693 f 1 SUS 0.229 < 17 F2 0.170 0.536 2.480 f 1 SUS 0.230 --- > 15 C9 0.117 1.500 1.582 c3 1 SUS 0.620 > 16 F1 1.056 2.097 1.693 f 1 SUS 0.228 > 17 F2 0.170 0.536 2.480 f 1 SUS 0.231 30c30 < 24 C11 1.919 0.369 0.836 ca 1 SUS 0.109 --- > 24 C11 1.919 0.369 0.836 ca 1 SUS 0.108 --------------------------------------- possible FAILURE: check DGN.mol2.dif /home/Debabrata/amber9/test/antechamber/guanine_amber 28c28 < 22 H21 1.963 -3.996 8.204 H 1 DGN 0.408 --- > 22 H21 1.963 -3.996 8.204 H 1 DGN 0.407 32c32 < 26 C3' 2.576 2.967 3.331 CT 1 DGN 0.120 --- > 26 C3' 2.576 2.967 3.331 CT 1 DGN 0.119 34c34 < 28 C2' 3.425 1.699 3.439 CT 1 DGN -0.148 --- > 28 C2' 3.425 1.699 3.439 CT 1 DGN -0.149 --------------------------------------- possible FAILURE: check mdout.jar.dif /home/Debabrata/amber9/test/jar 187c187 < Etot = -3528.1878 EKtot = 514.2873 EPtot = - 4042.4750 --- > Etot = -3528.1877 EKtot = 514.2873 EPtot = - 4042.4750 -----------------------------------------------------------------------------------------------------------------------------------------------------

On 12/3/06, Carlos Simmerling <carlos_at_csb.sunysb.edu> wrote: > > you need to give more detail such as which amber version you are using. > > Gobind Singh Bisht wrote: > > > dear users, > > Sander is not accepting the NOSHAKEMASK string that i > > entered in the input file. > > the input file is: > > > ------------------------------------------------------------------------------------------------------------- > > > > md equilibration for 100ps of energy minimised atpase > > &cntrl > > imin=0, > > ntx=1, > > ntpr=100, > > ntwx=100, > > nstlim=50000, > > dt=0.002, > > cut=12.0, > > ntb=0, > > igb=1, > > ntt=3, gamma_ln= 1.0, > > tempi=0.0, temp0=300.0, > > ntc=3, ntf=1, jfastw=4, > > > > > noshakemask=":2076-2086,2336-2346,2261-2266,1609-1619,1869-1879,1794-1799, > > 2530-2540,2790-2800,2715-2720,3268-3290,3210-3222", > > / > > > ----------------------------------------------------------------------------------------------------------------------------------- > > > > sander is giving the following error in the output file: > > ------------------------------------------------------------------------ > > Error in group input::atommask.f::tokenize > > illegal symbol in maskstr: > > ------------------------------------------------------------------------ > > Can anybody please help me figure out what wrong. > > thanx > > gobind > > ----------------------------------------------------------------------- > The AMBER Mail Reflector > To post, send mail to amber_at_scripps.edu > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu >

-- ---------------------------------------------------------------------------------------------------------------- Gobind Singh Bisht Btech III year (Biotechnology and Biochemical Engineering) Department Of Biotechnology IIT Kharagpur, Kharagpur-721302 West Bengal, India Ph No: +919932604909 Website: http://users.cjb.net/gobindbisht/ ----------------------------------------------------------------------------------------------------------------

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Next message: Ye Mei: "Re: AMBER: bugfix"
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AMBER Archive (2006)Subject: Re: AMBER: Problem with specifying NOSHAKEMASK

AMBER Archive (2006)
Subject: Re: AMBER: Problem with specifying NOSHAKEMASK