Re: [AMBER] COOH group troubling

From: Jio M <jiomm.yahoo.com>
Date: Sun, 6 Dec 2009 10:53:22 -0800 (PST)

Dear AMBER users;



Thanks for reply,



I am giving ligand mol2 file and its frcmod file obtained by parmchk



>It would probably help us out if you included the frcmod that you're using

>so we don't have to guess at what's going on, along with your mol2 or prep

>file for the custom ligand.



Here is mol2 file

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

.<TRIPOS>MOLECULE

MOL

   37    40     1     0     0

SMALL

resp





.<TRIPOS>ATOM

      1
C1         
3.5960    0.8310   -0.0240
cc        1
MOL      0.863085

      2
C2         
2.3150    1.2150   -0.0180
cd        1
MOL     -0.965274

      3
C3         
1.2210    0.2500   -0.0190
cd        1
MOL      0.446138

      4
C4         
1.5960   -1.1680   -0.0170
cd        1
MOL     -0.361520

      5
C5         
2.8710   -1.5870   -0.0200
cc        1
MOL      0.510971

      6
C6        
-0.0860    0.6000   -0.0330
cc        1
MOL      0.151491

      7
C7         -0.7470  
-1.7680   -0.0260
ca        1
MOL     -0.196705

      8
C8         -1.1330  
-0.4210   -0.0310
ca        1
MOL      0.450403

      9
C9         -2.4980  
-0.1300   -0.0330
ca        1
MOL     -0.836217

     10
H1        
-2.8230    0.8880   -0.0250
ha        1
MOL      0.214893

     11
C10        -3.4410  
-1.1420   -0.0350
ca        1
MOL      0.735201

     12
C11        -3.0320  
-2.4860   -0.0350
ca        1
MOL     -0.310150

     13
C12        -1.6710  
-2.8050   -0.0270
ca        1
MOL      0.592792

     14
H2         
2.0640    2.2530   -0.0030
ha        1
MOL      0.259497

     15
O1         
0.5810   -2.0930   -0.0180
os        1
MOL     -0.216186

     16
I1         
3.3850   -3.6220   -0.0210
i         1
MOL     -0.068227

     17
I2         -1.0530  
-4.8140   -0.0220
i         1
MOL     -0.064061

     18
I3         
5.1610    2.2450   -0.0200
i         1
MOL     -0.102804

     19
I4         -5.5020  
-0.6230   -0.0380
i         1
MOL     -0.034887

     20
C13         3.9840  
-0.6090   -0.0270
c         1
MOL      0.119328

     21
O2         
5.1570   -0.9550   -0.0350
o         1
MOL     -0.654444

     22
O3         -3.9020  
-3.5290   -0.0370
oh        1
MOL     -0.552747

     23
H3         -4.8320  
-3.3200   -0.0560
ho        1
MOL      0.303880

     24
C14        -0.5070   
2.0400   -0.0660 ca       
1 MOL      0.043872

     25
C15        -0.7190   
2.6980   -1.2770 ca       
1 MOL      0.205730

     26
C16        -0.7240   
2.7430    1.1200
ca        1
MOL     -0.489797

     27
C17        -1.1250   
4.0280   -1.3140 ca       
1 MOL      0.277710

     28
C18        -1.1310   
4.0700    1.0880
ca        1
MOL      0.319675

     29
C19        -1.3300   
4.7210   -0.1230 ca       
1 MOL      0.148373

     30
Cl1        -0.4610   
1.8010   -2.7940 cl       
1 MOL     -0.295239

     31
Cl2        -1.3800   
4.8420   -2.8700 cl       
1 MOL     -0.221770

     32
Cl3        -1.8430   
6.4190   -0.1510 cl       
1 MOL     -0.187134

     33
Cl4        -1.3730   
4.9290    2.6300
cl        1
MOL     -0.211557

     34
C20        -0.5020   
2.0540    2.4370
c         1
MOL      1.672474

     35
O4         
0.5780    1.8940    2.9560
o         1
MOL     -1.009309

     36
O5        
-1.6600    1.6100    2.9680
oh        1
MOL     -1.005568

     37
H4        
-1.5810    1.1910    3.8260
ho        1
MOL      0.468084

.<TRIPOS>BOND

     1    1    2 2  

     2    1   18 1  

     3    1   20 1  

     4    2    3 1  

     5    2   14 1  

     6    3    4 ar 

     7    3    6 ar 

     8    4    5 2  

     9    4   15 ar 

    10    5   16 1  

    11    5   20 1  

    12    6    8 ar 

    13    6   24 1  

    14    7    8 ar 

    15    7   13 ar 

    16    7   15 ar 

    17    8    9 ar 

    18    9   10 1  

    19    9   11 ar 

    20   11   12 ar 

    21   11   19 1  

    22   12   13 ar 

    23   12   22 1  

    24   13   17 1  

    25   20   21 2  

    26   22   23 1  

    27   24   25 ar 

    28   24   26 ar 

    29   25   27 ar 

    30   25   30 1  

    31   26   28 ar 

    32   26   34 1  

    33   27   29 ar 

    34   27   31 1  

    35   28   29 ar 

    36   28   33 1  

    37   29   32 1  

    38   34   35 2  

    39   34   36 1  

    40   36   37 1  

.<TRIPOS>SUBSTRUCTURE

     1
MOL         1
TEMP             
0 ****  ****    0 ROOT

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



here is frcmod obtained for this mol2 by parmchk



remark goes here

MASS



BOND

cc-i   223.20   2.153       same as c2-i



ANGLE

cd-cc-i    56.300     121.030   same as c2-c2-i

ca-cc-ca   63.800     117.930   same as ca-ce-ca

i -cc-c    20.403     118.410   Calculated with empirical approach



DIHE

cd-cd-os-ca   1   
1.050      
180.000          
2.000      same as X -c2-os-X

cd-cc-ca-ca   1   
2.550      
180.000          
2.000      same as X -c2-ca-X

cc-cd-os-ca   1   
1.050      
180.000          
2.000      same as X -c2-os-X

ca-ca-cc-ca   1   
2.550      
180.000          
2.000      same as X -c2-ca-X



IMPROPER

c -cd-cc-i         
1.1         
180.0        
2.0          Using default
value

cc-cd-cd-ha        
1.1         
180.0        
2.0          Using default
value

cc-cd-cd-cd        
1.1         
180.0        
2.0          Using default
value

cc-cd-cd-os        
1.1         
180.0        
2.0          Using default
value

ca-ca-cc-cd        
1.1         
180.0        
2.0          Using default
value

ca-ca-ca-os        
1.1         
180.0        
2.0          Using default
value

ca-ca-ca-cc        
1.1         
180.0        
2.0          Using default
value

ca-ca-ca-ha        
1.1         
180.0        
2.0          General
improper torsional angle (2 general atom types)

ca-ca-ca-oh        
1.1         
180.0        
2.0          Using default
value

cc-cc-c -o        
10.5         
180.0        
2.0          General
improper torsional angle (2 general atom types)

c -ca-ca-ca        
1.1         
180.0        
2.0          Using default
value

ca-o -c -oh       
10.5         
180.0        
2.0          General
improper torsional angle (2 general atom types)



NONBON

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



>>To be sure the COOH group is the problem, in your minimization .out

>>file, see which atom is reported for gradient max (GMAX).



 NSTEP      
ENERGY         
RMS           
GMAX        
NAME    NUMBER

    100     
-5.5260E+03     8.3251E+03    
5.8941E+05    
O4       1454



 BOND    =     
129.1156  ANGLE   =    
1460.1636  DIHED     
=      729.9489

 VDWAALS =    -2233.1513 
EEL     =     
131.4737  HBOND     
=        0.0000

 1-4 VDW =      373.4535  1-4 EEL
=    -6116.9878  RESTRAINT 
=        0.0000





   NSTEP      
ENERGY         
RMS           
GMAX        
NAME    NUMBER

    150     
-5.4068E+07     2.8399E+11    
1.6160E+13    
H4       1456



 BOND    =     
127.7585  ANGLE   =    
1459.8293  DIHED     
=      728.7389

 VDWAALS =    -2233.1303 
EEL     =     
131.5763  HBOND     
=        0.0000

 1-4 VDW =      373.4517  1-4 EEL =
*************  RESTRAINT 
=        0.0000







Atom correspond to either H(H4) or O(O5) of OH or O(O4) of C=O.





thanks and regards;

JIomm




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Received on Sun Dec 06 2009 - 11:00:02 PST
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