[gmx-users] Re: gmx-users Digest, Vol 114, Issue 15
Hari Pandey
harichem12 at yahoo.com
Tue Oct 29 00:41:58 CET 2013
Thank you so much Mark.
I still did not understand. More detaily. Atomtypes are only following:
atomtypes.atp::
H 1.00800 ; polar H
DUM 0.00000 ; dummy atom
HAL1 1.008000 ; alphatic proton
HAL2 1.008000 ; alphatic proton
HAL3 1.008000 ; alphatic proton
CTL1 12.011000 ; carbonyl C (acetic acid/methyl acetate);;;;;;;;;;;
CTL1 12.011000 ; sp3 carbon with 1 H (-CH1-)
CTL2 12.011000 ; carbon of methylene group (-CH2-)
CTL3 12.011000 ; carbon of methyl group (-CH3)
OBL 15.999400 ; acetic acid carboxyl oxygen (e. to protein OB)
OCL 15.999400 ; acetate oxygen
OSL 15.999400 ; ester oxygen
O2L 15.999400 ; Nucleic acid =O in phosphate or sulfate
SL 32.060000 ; Sulfate sulfur
NA 22.989770 ; FOR sodium ion
MR.rtp:
S SL 1.3600 0
OS1 O2L -0.6000 0
OS2 O2L -0.6000 0
OS3 O2L -0.6000 0
C1 CTL1 -0.1900 0
H1 HAL1 0.0900 0
C2 CTL2 -0.1800 1
H2 HAL2 0.0900 1
H3 HAL2 0.0900 1
C3 CL 0.6300 2 ;;;;;;;;;;;;;;;;;
O1 OBL -0.5200 2
O2 OSL -0.3400 2
C4 CTL2 -0.1800 3
H4 HAL2 0.0900 3
H5 HAL2 0.0900 3
C5 CTL1 -0.0900 4
H6 HAL1 0.0900 4
C6 CTL2 -0.1800 5
H7 HAL2 0.0900 5
H8 HAL2 0.0900 5
C7 CTL2 -0.1800 6
H9 HAL2 0.0900 6
H10 HAL2 0.0900 6
C8 CTL2 -0.1800 7
H11 HAL2 0.0900 7
H12 HAL2 0.0900 7
C9 CTL3 -0.2700 8
H13 HAL3 0.0900 8
H14 HAL3 0.0900 8
H15 HAL3 0.0900 8
C10 CTL2 -0.1800 9
H16 HAL2 0.0900 9
H17 HAL2 0.0900 9
C11 CTL3 -0.2700 10
H18 HAL3 0.0900 10
H19 HAL3 0.0900 10
H20 HAL3 0.0900 10
C12 CL 0.6300 11 ;;;;;
O3 OBL -0.5200 11
O4 OSL -0.3400 11
C13 CTL2 -0.1800 12
H21 HAL2 0.0900 12
H22 HAL2 0.0900 12
C14 CTL1 -0.0900 13
H23 HAL1 0.0900 13
C15 CTL2 -0.1800 14
H24 HAL2 0.0900 14
H25 HAL2 0.0900 14
C16 CTL2 -0.1800 15
H26 HAL2 0.0900 15
H27 HAL2 0.0900 15
C17 CTL2 -0.1800 16
I have A.pdb and I got A.gro using this force field.
Some part of A.pdb::
REMARK Created: Fri Jun 08 12:50:20 Paris, Madrid (heure d'?t?) 2007
CRYST1 8.760 8.760 8.760 90.00 90.00 90.00 P1 1
MODEL 1
ATOM 1 S AOT 151 6.864 -6.902 0.078 1.00 0.00
ATOM 2 OS1 AOT 151 7.820 -5.791 -0.815 1.00 0.00
ATOM 3 OS2 AOT 151 5.369 -7.134 -0.714 1.00 0.00
ATOM 4 OS3 AOT 151 6.589 -6.277 1.657 1.00 0.00
ATOM 5 C1 AOT 151 7.728 -8.482 0.196 1.00 0.00
ATOM 6 H1 AOT 151 8.702 -8.326 0.676 1.00 0.00
ATOM 7 C2 AOT 151 7.952 -8.937 -1.268 1.00 0.00
ATOM 8 H2 AOT 151 7.067 -9.120 -1.697 1.00 0.00
ATOM 9 H3 AOT 151 8.423 -8.212 -1.771 1.00 0.00
ATOM 10 C3 AOT 151 6.874 -9.526 1.026 1.00 0.00
ATOM 11 O1 AOT 151 6.661 -9.024 2.356 1.00 0.00
ATOM 12 O2 AOT 151 7.505 -10.821 1.169 1.00 0.00
ATOM 13 C4 AOT 151 6.679 -11.663 1.968 1.00 0.00
ATOM 14 H4 AOT 151 5.837 -11.877 1.473 1.00 0.00
ATOM 15 H5 AOT 151 6.454 -11.200 2.825 1.00 0.00
ATOM 16 C5 AOT 151 7.443 -12.948 2.264 1.00 0.00
ATOM 17 H6 AOT 151 8.370 -12.683 2.786 1.00 0.00
ATOM 18 C6 AOT 151 6.520 -13.788 3.227 1.00 0.00
ATOM 19 H7 AOT 151 5.703 -14.049 2.713 1.00 0.00
ATOM 20 H8 AOT 151 6.258 -13.205 3.996 1.00 0.00
ATOM 21 C7 AOT 151 7.156 -15.071 3.796 1.00 0.00
ATOM 22 H9 AOT 151 7.386 -15.690 3.045 1.00 0.00
ATOM 23 H10 AOT 151 7.987 -14.835 4.300 1.00 0.00
ATOM 24 C8 AOT 151 6.164 -15.763 4.742 1.00 0.00
ATOM 25 H11 AOT 151 5.919 -15.140 5.485 1.00 0.00
ATOM 26 H12 AOT 151 5.341 -16.019 4.236 1.00 0.00
ATOM 27 C9 AOT 151 6.825 -17.024 5.323 1.00 0.00
ATOM 28 H13 AOT 151 6.186 -17.482 5.941 1.00 0.00
ATOM 29 H14 AOT 151 7.649 -16.767 5.828 1.00 0.00
ATOM 30 H15 AOT 151 7.071 -17.645 4.579 1.00 0.00
ATOM 31 C10 AOT 151 7.781 -13.600 0.859 1.00 0.00
ATOM 32 H16 AOT 151 8.245 -12.909 0.305 1.00 0.00
ATOM 33 H17 AOT 151 6.914 -13.847 0.427 1.00 0.00
ATOM 34 C11 AOT 151 8.675 -14.865 0.885 1.00 0.00
ATOM 35 H18 AOT 151 8.819 -15.191 -0.049 1.00 0.00
ATOM 36 H19 AOT 151 8.226 -15.580 1.422 1.00 0.00
ATOM 37 H20 AOT 151 9.557 -14.642 1.299 1.00 0.00
ATOM 38 C12 AOT 151 8.787 -10.187 -1.298 1.00 0.00
ATOM 39 O3 AOT 151 8.970 -10.608 -2.647 1.00 0.00
ATOM 40 O4 AOT 151 10.052 -9.886 -0.718 1.00 0.00
ATOM 41 C13 AOT 151 10.844 -11.080 -0.668 1.00 0.00
ATOM 42 H21 AOT 151 10.425 -11.731 -0.035 1.00 0.00
ATOM 43 H22 AOT 151 10.892 -11.486 -1.581 1.00 0.00
ATOM 44 C14 AOT 151 12.263 -10.738 -0.185 1.00 0.00
ATOM 45 H23 AOT 151 12.192 -10.271 0.810 1.00 0.00
ATOM 46 C15 AOT 151 12.814 -9.668 -1.245 1.00 0.00
ATOM 47 H24 AOT 151 12.813 -10.118 -2.138 1.00 0.00
ATOM 48 H25 AOT 151 12.165 -8.908 -1.254 1.00 0.00
ATOM 49 C16 AOT 151 14.233 -9.049 -1.05
The I run "editconf" which gives me wrong mass and density.
I am worried because
So please let me know what can I do to correct this.
How do I get "mass of input " correct?
The mass of input deviate large from actual.
I am writing again: editconf -c -f A.gro -o A.gro -density 1000 -bt cubic -box 5 -d 0.1 .
The mass of input displayed by GROMACS is 967 but actual mass is 444 in a.m.u
Thanks for your help
More information about the gromacs.org_gmx-users
mailing list