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


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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