[gmx-users] "editconf" displays incorrect mass of input, GROMACS version 4.5.4
Hari Pandey
harichem12 at yahoo.com
Wed Oct 30 19:34:56 CET 2013
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 4.5.4. I tested 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)
More information about the gromacs.org_gmx-users
mailing list