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openforcefield / amber-ff-porting

Scratch space for porting amber FFs into SMIRNOFF format
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C-terminal PRO.mol2 is created with incorrect partial charges #9

Open j-wags opened 4 years ago

j-wags commented 4 years ago

In the course of debugging #2, I noticed that the partial charges on CTerminal/PRO/PRO.mol2 are kinda weird [1]. This may be related to an error message that pops up during system generation [2].

[1]

(off-dev) jeffreywagner@JW-MBP$ cat PRO.mol2 
@<TRIPOS>MOLECULE
default_name
   21    21     1     0     0
SMALL
No Charge or Current Charge

@<TRIPOS>ATOM
      1 H1          26.0920    24.8880    24.0010 H          1 ACE       0.112300
      2 CH3         25.9970    25.9720    24.0070 C.3        1 ACE      -0.366200
      3 H2          25.6220    26.2960    24.9760 H          1 ACE       0.112300
      4 H3          25.3290    26.2900    23.2110 H          1 ACE       0.112300
      5 C           27.3720    26.5810    23.7870 C.2        1 ACE       0.597200
      6 O           28.2780    25.8270    23.4420 O.2        1 ACE      -0.567900
      7 N           27.5140    27.9110    23.9390 N.am       2 CPR      -0.567900
      8 CD          26.4410    28.8820    24.0610 C.3        2 CPR      -0.567900
      9 HD2         26.2330    29.0550    25.1180 H          2 CPR      -0.567900
     10 HD3         25.5380    28.5690    23.5390 H          2 CPR      -0.567900
     11 CG          26.9990    30.1490    23.4240 C.3        2 CPR      -0.567900
     12 HG2         26.4950    31.0430    23.7910 H          2 CPR      -0.567900
     13 HG3         26.9210    30.0770    22.3380 H          2 CPR      -0.567900
     14 CB          28.4690    30.1130    23.8390 C.3        2 CPR      -0.567900
     15 HB2         28.5800    30.6140    24.8030 H          2 CPR      -0.567900
     16 HB3         29.1070    30.5910    23.0950 H          2 CPR      -0.567900
     17 CA          28.8000    28.6180    23.9820 C.3        2 CPR      -0.567900
     18 HA          29.4170    28.2960    23.1440 H          2 CPR      -0.567900
     19 C           29.5880    28.3690    25.2780 C.2        2 CPR      -0.567900
     20 O           28.9360    28.2350    26.3400 O.co2      2 CPR      -0.567900
     21 OXT         30.8350    28.4020    25.1910 O.co2      2 CPR      -0.567900
@<TRIPOS>BOND
     1     5     6 2   
     2     5     7 am  
     3     2     3 1   
     4     2     4 1   
     5     2     5 1   
     6     1     2 1   
     7    19    20 1   
     8    19    21 1   
     9    17    18 1   
    10    17    19 1   
    11    14    15 1   
    12    14    16 1   
    13    14    17 1   
    14    11    12 1   
    15    11    13 1   
    16    11    14 1   
    17     8     9 1   
    18     8    10 1   
    19     8    11 1   
    20     7     8 1   
    21     7    17 1   
@<TRIPOS>SUBSTRUCTURE
     1 ACE         1 TEMP              0 ****  ****    0 ROOT

[2] 

(off-dev) jeffreywagner@JW-MBP$ . GenerateSystems.sh 
PRO PRO
PRO PRO
/Users/jeffreywagner/miniconda3/envs/off-dev/bin/tleap: line 10: 95955 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
PRO PRO
/Users/jeffreywagner/miniconda3/envs/off-dev/bin/tleap: line 10: 95992 Abort trap: 6           $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep -I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd $*
j-wags commented 4 years ago

I'm removing the essential-for-MVP tag, since this appears to only affect the mol2, and not the prmtop. So, this issue is cosmetic.