[gmx-users] Re: gmx-users Digest, Vol 114, Issue 15
Justin Lemkul
jalemkul at vt.edu
Tue Oct 29 01:15:16 CET 2013
On 10/28/13 8:07 PM, Hari Pandey wrote:
> Many thanks to Dr.Lemkul
>
> Yes mass is 444 in my .top file and I did "-density 1000 " because then it
> will show the density also.
>
If you have one molecule in a box of a known size, you don't need any
command-line flags - you have a mass and a known volume. Using -density 1000 is
probably harmless, since it is the default, but you can remove that level of
complexity in the command (because, again, you are doing things that conflict).
> I am wandering how do I find that which atom name mismatched. The
> forcefield folder is in my working directory and there are all files.
> atomtypes.atp is there and which contains the atom names which I posted last email
Hard to say. Your input snippets are incomplete. A rough calculation of the
.rtp file gives me a mass of only 375 amu, so I don't know where 444 is coming
from and it's impossible to tell if you haven't shown us everything or if there
are mistakes somewhere else.
-Justin
> Thanks for your regard
> Hari
>
>
> On Monday, October 28, 2013 4:50 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 10/28/13 7:41 PM, Hari Pandey wrote:
> >
> >
> >
> >
> > 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
> >
>
> There are several inconsistencies here, not the least of which is that the .rtp
> and coordinates do not match. It appears that something has gotten cut off in
> the copy-paste process.
>
> > 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 topology is correct. Whatever editconf says has little relevance, in my
> experience.
>
> > 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 .
>
> This command line is doing several things simultaneously that potentially
> conflict and you're trying to make a single molecule scale its coordinates to
> have a density of 1000. This doesn't make much sense. What are you trying to
> achieve?
>
>
> > The mass of input displayed by GROMACS is 967 but actual mass is 444 in a.m.u
>
> >
>
> If 444 is in the topology and 444 is what is correct, then that's all that
> really matters because only the topology is relevant for dynamics. There's
> probably some atom name mismatch that editconf is not picking up correctly
> (hence why I noted the incompleteness above) and the WARNING that is printed to
> indicate this fact.
>
> -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 <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
>
>
> ==================================================
>
>
--
==================================================
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
==================================================
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