[gmx-users] (no subject)

[Hari Pandey]

Dear Gromacs users,
Please somebody help .
editconf computs the incorrect value of  "mass of input".  I tried to resolve this problem but failed. Previously I was doing AOt but now I just found that the molecule OS1 =O2L  showing error . Here I posted my A.pdb, RM.rtp atomtypes.atp.  The mass of input  should be 15.99940  but it showing 222. Please help me whether this is bug or something wrong with my GROMACS. Its GROMACS version 5.4.5. I calculate for just 1 atom to see error

I have just 1  atom in my pdb  so only on  in .rtp too
A.pdb
CRYST1   12.000   12.000   12.000  90.00  90.00  90.00 P 1         1
 MODEL        1 
ATOM       1  OS1    AOT   151       7.820  -5.791  -0.815  1.00  0.00           O 
ENDMDL
TER

RM.rtp
[AOT ] ;
 [ atoms ]
        OS1     O2L     -0.6000         1
  [ bonds ]

atomtypes.atp
NTL     14.007000 ;     ammonium nitrogen
NH3L    14.007000 ;     nitrogen phosphatidylethanolamine
OBL     15.999400 ;     acetic acid carboxyl oxygen (e. to protein OB)
OCL     15.999400 ;     acetate oxygen
OSL     15.999400 ;     ester oxygen
OSLP    15.999400 ;     Phosphate oxygen, to avoid conflict with methylacetate type O
O2L     15.999400 ;     Nucleic acid =O in phosphate or sulfate
OHL     15.999400 ;     Nucleic acid phosphate hydroxyl oxygen
PL      30.974000 ;     phosphorus
SL      32.060000 ;     Sulfate sulfur
SOD     22.989770 ;     Sodium Ion
MG      24.305000 ;     Magnesium Ion

OUTPUT OF editconf

Volume  of input 125 (nm^3)
Mass    of input 222.295 (a.m.u.)   This is incorrect, even to much incorrect. It should be 15.999940
Density of input 2.95304 (g/l)
Scaling all box vectors by 0.143468
new system size :  0.000  0.000  0.000
    shift       :  2.141  2.141  2.141 (nm)
new center      :  2.500  2.500  2.500 (nm)
new box vectors :  5.000  5.000  5.000 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 125.00               (nm^3)

Many Many Thanks for your help
Hari