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
MODEL1
ATOM 1 OS1AOT 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
NH3L14.007000 ; nitrogen phosphatidylethanolamine
OBL 15.999400 ; acetic acid carboxyl oxygen (e. to protein OB)
OCL 15.999400 ; acetate oxygen
OSL 15.999400 ; ester oxygen
OSLP15.999400 ; 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 32.06 ; Sulfate sulfur
SOD 22.989770 ; Sodium Ion
MG 24.305000 ; Magnesium Ion
OUTPUT OF editconf
Volume of input 125 (nm^3)
Massof input 222.295 (a.m.u.) This is incorrect, even to much incorrect.
It should be 15.40
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)
Massof 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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
