Hello there,
During 'make test' for AT 1.4 'sleap' seemed OK. However, using on a real
case and I have this issue:
sleap
[gtkleap]$ source leaprc.ff99bsc0
[gtkleap]$
[gtkleap]$ source leaprc.gaff
Info: ignoring unknown atom type: cz
Info: while reading BOND. Input: cz nh 487.8 1.3391 SOURCE4
32 0.0045
Info: ignoring unknown atom type: Si
Info: while reading BOND. Input: Si c3 189.8 1.8928 SOURCE4
77 0.0061
Info: ignoring unknown atom type: Si
Info: while reading BOND. Input: Si ca 191.1 1.8898 SOURCE4
11 0.0028
Info: ignoring unknown atom type: Si
Info: while reading BOND. Input: Si ha 186.3 1.4887 SOURCE4
6 0.0040
Info: ignoring unknown atom type: Si
Info: while reading BOND. Input: Si oh 267.6 1.6792 SOURCE4
6 0.0035
Info: ignoring unknown atom type: Si
Info: while reading BOND. Input: Si os 287.7 1.6524 SOURCE4
22 0.0057
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: Si c3 c3 74.610 114.340 SOURCE4
26 1.1613
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: Si c3 h1 51.040 110.900 SOURCE4
17 1.0270
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: Si c3 hc 50.960 111.210 SOURCE4
222 0.4865
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: Si ca ca 73.850 121.430 SOURCE4
19 0.4235
Info: ignoring unknown atom type: h
Info: while reading ANGL. Input: f c h 0.000 109.900 SOURCE2
1 0.0000
Info: ignoring unknown atom type: h
Info: while reading ANGL. Input: h c o 0.000 127.300 SOURCE2
1 0.0000
Info: ignoring unknown atom type: cz
Info: while reading ANGL. Input: nh cz nh 72.970 120.170 SOURCE4
26 0.3964
Info: ignoring unknown atom type: cz
Info: while reading ANGL. Input: c3 nh cz 63.010 125.510 SOURCE4
12 0.5177
Info: ignoring unknown atom type: cz
Info: while reading ANGL. Input: cz nh hn 48.790 121.240 SOURCE4
40 0.5682
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: Si oh ho 52.570 115.710 SOURCE4
5 0.1738
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: Si os c3 74.830 124.640 SOURCE4
9 0.2879
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: c3 Si c3 34.810 109.820 SOURCE4
88 0.5569
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: c3 Si ca 34.800 110.090 SOURCE4
26 0.7331
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: c3 Si oh 38.160 107.440 SOURCE4
8 1.5150
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: c3 Si os 38.140 108.750 SOURCE4
38 0.7301
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: ha Si ha 19.530 108.770 SOURCE4
5 0.5372
Info: ignoring unknown atom type: Si
Info: while reading ANGL. Input: os Si os 42.630 108.350 SOURCE4
15 1.7995
Info: ignoring unknown atom type: cb
Info: while reading DIHE. Input: X c1 cb X 2 0.000 180.000
2.000
Info: ignoring unknown atom type: cb
Info: while reading DIHE. Input: X n1 cb X 2 0.000 180.000
2.000
[gtkleap]$ set default fastbld on
[gtkleap]$ dmp = loadpdb /Users/alan/Programmes/dmp.pdb
Warning: cannot find template for residue DMP in our library.
I am going to construct the template by myself.
OK. I have fixed bond order and added hydrogens.
Now I am calling antechamber to assign atom type and partial
charge.
Total number of electrons: 302; net charge: 0
Running: /Users/alan/Programmes/amber11/bin/sqm -O -i sqm.in -o sqm.out
Error: sparm type does not exist!
calling "mdlize_mdb( )"
calling "mdlize_resd_bymdb( )"
[gtkleap]$
Testing with AT 1.2 (amber10 folder) and it worked fine.
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Received on Wed Apr 28 2010 - 12:00:03 PDT
