[gmx-users] "editconf" displays incorrect mass of input, GROMACS version 4.5.4

[Justin Lemkul]

On 10/30/13 2:34 PM, Hari Pandey wrote:
> 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)
>

I cannot reproduce the problem with 4.6.3.  I get correct output:

Volume  of input 1.728 (nm^3)
Mass    of input 15.9994 (a.m.u.)
Density of input 15.3748 (g/l)
Scaling all box vectors by 0.248658
new system size :  0.000  0.000  0.000
     shift       :  2.326  2.480  2.480 (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)

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================