Re: [gmx-users] trjcat after trjconv
Yes. Cheers, Tsjerk On Fri, Sep 27, 2013 at 7:51 AM, Venkat Reddy venkat...@gmail.com wrote: Thanks for the quick reply sir. So, does it mean I can apply trjcat on the processed xtc files??? On Thu, Sep 26, 2013 at 10:25 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Venkat, These options are 'frame intrinsic' or 'history independent', unlike -pbc nojump. Cheers, Tsjerk On Sep 26, 2013 6:46 PM, Venkat Reddy venkat...@gmail.com wrote: Dear Tsjerk sir, I used trjconv -pbc mol -ur compact options. On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Venkat, It... -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g... -- 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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
Re: [gmx-users] trjcat after trjconv
Thank you sir. On Fri, Sep 27, 2013 at 11:47 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: Yes. Cheers, Tsjerk On Fri, Sep 27, 2013 at 7:51 AM, Venkat Reddy venkat...@gmail.com wrote: Thanks for the quick reply sir. So, does it mean I can apply trjcat on the processed xtc files??? On Thu, Sep 26, 2013 at 10:25 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Venkat, These options are 'frame intrinsic' or 'history independent', unlike -pbc nojump. Cheers, Tsjerk On Sep 26, 2013 6:46 PM, Venkat Reddy venkat...@gmail.com wrote: Dear Tsjerk sir, I used trjconv -pbc mol -ur compact options. On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Venkat, It... -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g... -- 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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
[gmx-users] principal component analysis
Dear all gmx users I would like to calculate pc loadings for various integrated factors in the form of following sample table: Integrated factorsPC1PC2PC3 PC4PC5PC6PC7PC8 PC9PC10Total nonpolar surface area0.60 -0.07-0.76-0.11-0.060.11 0.05-0.160.06-0.02Chain exposed area 0.92 -0.14-0.050.12 0.230.200.09-0.07-0.03 0.08Chain buried area0.74-0.30-0.41 0.120.240.260.05 0.03-0.060.21Chain unpolar exposed area 0.71-0.08-0.630.02 0.03 0.280.00-0.060.08-0.03 Chain unpolar buried area0.69-0.23-0.580.06 0.12 0.17-0.100.20-0.16 -0.01Main chain B factor0.120.77-0.06 0.62-0.01-0.01-0.080.01 0.050.04Side chain B factor0.07 0.74-0.050.66-0.01 0.01-0.030.000.100.01Whole chain B factor 0.090.75-0.050.64 -0.010.00-0.050.010.08 0.02Average number of cavities-0.02 -0.43 0.72-0.090.340.10-0.19 0.170.310.09Average volume of cavity -0.040.14 0.63-0.47-0.48 0.350.020.11-0.010.06 Content of Helix 0.870.090.00-0.41 0.17 -0.10-0.09-0.12 0.130.00and so on.. Please suggest me the way to proceed. I have done cartesian principal component analysis using g_covar -f *.xtc -s *.tpr and using g_anaeig This way I could get principal components. But then how to dissect each pc in terms of above integrated factors? Any help is appreciated. -- 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
[gmx-users] Re: Re: calculating dihedral properties
Dear Justin,
sorry for the late answer and acknowledgements... Please see below my
comments.
Anna
__
Anna Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via Giovanni Paolo II, 132
84084 Fisciano (SA)
Italy
Phone: +39 089 969583
Fax: +39 089 969603
E-mail: amarabo...@unisa.it
Skype: annam1972
Web page: http://www.unisa.it/docenti/annamarabotti/index
Indifference is the eighth deadly sin (don Andrea Gallo)
Dear all,
I would like to calculate how three dihedrals in my
protein are evolving during the simulation time, but I don't understand
which is the correct command to do.
In particular, I would like to
know:
- what is the value of a specified dihedral (in degrees)
- if
this value changes during the time of simulation
- what is the
probability distribution of this angle.
In order to answer to these
questions, first, I created an index file with make_ndx, in which I set
the three dihedrals of my interest by selecting the atoms of the
dihedrals. Then I used the command G_ANGLE -F PROT.XTC -N PROT.NDX -TYPE
DIHEDRAL -OD PROT_DIHDIST.XVG -OV PROT_DIHAVER.XVG -OT
PROT_DIHTRANS4.XVG -OH PROT_TRHISTO.XVG -OC PROT_DIHCORR.XVG
Then, I
had a look at the results, but I really don't understand them...in any
case, they are not what I was expected to find. I was expecting to find
somewhere a graph in which on the X axis I have the time, and on the Y
axis the oscillation of the angle around an average value, expressed in
degrees. Moreover, I was expecting to create a graph with a
Gaussian-like shape, indicating what is the most frequent value assumed
by this dihedral during my simulation. None of the resulting graphs
appear like that.
It would be helpful to see images of what you've got, but I suspect it all comes
down to the fact that you're analyzing multiple dihedrals without using the -all
option. Per the second paragraph of g_angle -h:
With option -ov, you can plot the average angle of a group of angles as a
function of time. With the -all option, the first graph is the average and
the rest are the individual angles.
The -od output should give you the distribution, but I can't envision what you
got as output.
I've tried to attach here the files with the images, but the message was
filtered out. Please let me know how can I send you the
images. Please take into account that with g_angle command I'm not
analysing multiple dihedrals (or at least, this is not what I'm intended
to do): using the index file .ndx I told Gromacs to analyse a
particular dihedral that I defined using a list of the four atoms
composing it. Then, to analyse the three dihedrals of my interest, I
launched three times the command g_angle, and every time I selected a
different dihedral to analyse.
In any case, I repeated the command using the -all flag as suggested,
but nothing changed.
Another strange thing is that the dihedral variation is still between
two fixed values (-200 and 200) instead of 0-360 as I expected to be. Is
this another possible bug or not?
Finally, I used g_sgangle in order to understand if,
during the simulation, the distance and the angle between two aromatic
residues varies during the time. In the case of the angle variation, the
values on the Y axis of the resulting graph vary in all cases between -1
and 1. On the Y axis the legend states Angle(degrees) but it seems
very strange to me that all my dihedrals are set on this very narrow
range of values.
I think that's a small output labeling bug. If the range is {-1..1} then it's
probably the cosine of the angle, not the angle itself, but IIRC the angle is
listed in the second column of the .xvg file.
Indeed, when I used xmgrace -nxy, the correct angle value appeared in
the graph. Thanks a lot.
-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
--
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Re: [gmx-users] principal component analysis
Hi Pratibha, The table is all garbled, and your description insufficiently clear for us to form a mental picture of what you want, what you've tried to get that, where it goes wrong, or where you get stuck, and how we can help you on the right track again. Cheers, Tsjerk On Fri, Sep 27, 2013 at 2:03 PM, pratibha kapoor kapoorpratib...@gmail.comwrote: Dear all gmx users I would like to calculate pc loadings for various integrated factors in the form of following sample table: Integrated factorsPC1PC2PC3 PC4PC5PC6PC7PC8 PC9PC10Total nonpolar surface area0.60 -0.07-0.76-0.11-0.060.11 0.05-0.160.06-0.02Chain exposed area 0.92 -0.14-0.050.12 0.230.200.09-0.07-0.03 0.08Chain buried area0.74-0.30-0.41 0.120.240.260.05 0.03-0.060.21Chain unpolar exposed area 0.71-0.08-0.630.02 0.03 0.280.00-0.060.08-0.03 Chain unpolar buried area0.69-0.23-0.580.06 0.12 0.17-0.100.20-0.16 -0.01Main chain B factor0.120.77-0.06 0.62-0.01-0.01-0.080.01 0.050.04Side chain B factor0.07 0.74-0.050.66-0.01 0.01-0.030.000.100.01Whole chain B factor 0.090.75-0.050.64 -0.010.00-0.050.010.08 0.02Average number of cavities-0.02 -0.43 0.72-0.090.340.10-0.19 0.170.310.09Average volume of cavity -0.040.14 0.63-0.47-0.48 0.350.020.11-0.010.06 Content of Helix 0.870.090.00-0.41 0.17 -0.10-0.09-0.12 0.130.00and so on.. Please suggest me the way to proceed. I have done cartesian principal component analysis using g_covar -f *.xtc -s *.tpr and using g_anaeig This way I could get principal components. But then how to dissect each pc in terms of above integrated factors? Any help is appreciated. -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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
Re: [gmx-users] Re: Re: calculating dihedral properties
On 9/27/13 8:18 AM, Anna Marabotti wrote: Dear Justin, sorry for the late answer and acknowledgements... Please see below my comments. Anna __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Giovanni Paolo II, 132 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 Web page: http://www.unisa.it/docenti/annamarabotti/index Indifference is the eighth deadly sin (don Andrea Gallo) Dear all, I would like to calculate how three dihedrals in my protein are evolving during the simulation time, but I don't understand which is the correct command to do. In particular, I would like to know: - what is the value of a specified dihedral (in degrees) - if this value changes during the time of simulation - what is the probability distribution of this angle. In order to answer to these questions, first, I created an index file with make_ndx, in which I set the three dihedrals of my interest by selecting the atoms of the dihedrals. Then I used the command G_ANGLE -F PROT.XTC -N PROT.NDX -TYPE DIHEDRAL -OD PROT_DIHDIST.XVG -OV PROT_DIHAVER.XVG -OT PROT_DIHTRANS4.XVG -OH PROT_TRHISTO.XVG -OC PROT_DIHCORR.XVG Then, I had a look at the results, but I really don't understand them...in any case, they are not what I was expected to find. I was expecting to find somewhere a graph in which on the X axis I have the time, and on the Y axis the oscillation of the angle around an average value, expressed in degrees. Moreover, I was expecting to create a graph with a Gaussian-like shape, indicating what is the most frequent value assumed by this dihedral during my simulation. None of the resulting graphs appear like that. It would be helpful to see images of what you've got, but I suspect it all comes down to the fact that you're analyzing multiple dihedrals without using the -all option. Per the second paragraph of g_angle -h: With option -ov, you can plot the average angle of a group of angles as a function of time. With the -all option, the first graph is the average and the rest are the individual angles. The -od output should give you the distribution, but I can't envision what you got as output. I've tried to attach here the files with the images, but the message was filtered out. Please let me know how can I send you the images. Please take into account that with g_angle command I'm not You need to upload images to public sharing sites and provide a URL. analysing multiple dihedrals (or at least, this is not what I'm intended to do): using the index file .ndx I told Gromacs to analyse a particular dihedral that I defined using a list of the four atoms composing it. Then, to analyse the three dihedrals of my interest, I launched three times the command g_angle, and every time I selected a different dihedral to analyse. OK, that sounds a lot different from the initial report :) Makes sense. In any case, I repeated the command using the -all flag as suggested, but nothing changed. Can you please show us what this means? A snippet of output here would be useful. Another strange thing is that the dihedral variation is still between two fixed values (-200 and 200) instead of 0-360 as I expected to be. Is this another possible bug or not? No, that's not a bug. Dihedrals can range equivalently from -180 to 180 or 0 to 360. Given that (I believe) the code deals in terms of the cosine of angles, the -180 to 180 range is intuitive. You can easily perform a simple transformation if you prefer that the values fall within the 0 to 360 range. -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
Re: [gmx-users] Membrane simulation with OPLS ff.
On 26 Sep, 2013, at 19:50, Justin Lemkul wrote: On 9/26/13 10:47 PM, Christopher Neale wrote: Dear Karthi: As far as I am aware, there is no OPLSAA lipid force field. I have used Berger lipids with OPLSAA protein ( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but that is mixing a UA lipid with an AA protein so be aware of possible problems arising out of that. There are OPLS-compatible lipids, though they are UA, but specifically designed to be used with OPLS-AA: dx.doi.org/10.1021/ct900086b I have not seen these parameters used very widely, though. I have used the Ulmschneider lipids quite a bit and they are working well for me. You can obtain them from Lipidbook, http://lipidbook.bioch.ox.ac.uk/ , in the browser http://lipidbook.bioch.ox.ac.uk/package/ select OPLS and Gromacs. Specifically, POPC is http://lipidbook.bioch.ox.ac.uk/package/show/id/52.html Oliver -- Oliver Beckstein * oliver.beckst...@asu.edu http://becksteinlab.physics.asu.edu/ Arizona State University Department of Physics Tempe, AZ 85287-1504 USA Office: PSF 348 Phone: +1 (480) 727-9765 FAX: +1 (480) 965-4669 Department of Physics: http://physics.asu.edu/home/people/faculty/oliver-beckstein Center for Biological Physics: http://biophysics.asu.edu/CBP/person.php?ID=343 -- 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
[gmx-users] ionomer topolgy
Hello Gromacs users, I am the beginner in Gromacs. I want to simulate ionomer in water. I could not find a pdb file for my case, and I tried to draw the ionomer in Avogadro software and generated the pdb file. However, gmx cannot find my residue names. I added my residue name to residuetypes.dat and added the residue in aminoacids.rtp in gromos. I does not work and it cannot find my new residue. What should I do? I also have some question regarding the .rtp file. Do you I need to include [ bonds] , [angles], [dihedrals] as well? How can I find charge and charge groups in the [ atoms] section. Thanks you -- 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
Re: [gmx-users] ionomer topolgy
On 9/27/13 2:34 PM, Ehsan Sadeghi wrote: Hello Gromacs users, I am the beginner in Gromacs. I want to simulate ionomer in water. I could not find a pdb file for my case, and I tried to draw the ionomer in Avogadro software and generated the pdb file. However, gmx cannot find my residue names. I added my residue name to residuetypes.dat and added the residue in aminoacids.rtp in gromos. I does not work and it cannot find my new residue. What should I do? Well, there are several Gromos parameter sets; have you modified and then chosen the correct one? In the absence of more detail, it's hard to figure out what's gone wrong. I also have some question regarding the .rtp file. Do you I need to include [ bonds] , [angles], [dihedrals] as well? How can I find charge and charge groups in the [ atoms] section. You need to at least specify [bonds], from which the angles and dihedrals can be generated. If you have planar groups, you need to specify [impropers] for them. Parametrization methods vary by force field, but if you're using a Gromos parameter set, most of the functional groups should be easily transferable to new species. If you are dealing with something totally new, then you need to derive the charges yourself. Details should be available in the primary literature for whatever parameter set you've chosen, as well as publications by others. Prepare to invest some time here; it's not necessarily trivial to derive the new values. -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
Re: [gmx-users] ionomer topolgy
Many thanks Justin. Here is my .pdb file: ATOM 1 C LIG 1 -10.450 5.214 -1.717 1.00 0.00 C ATOM 2 C LIG 1 -8.424 5.477 -1.030 1.00 0.00 C ATOM 3 C LIG 1 -6.603 5.864 -0.166 1.00 0.00 C ATOM 4 F LIG 1 -6.651 6.230 -1.691 1.00 0.00 F ATOM 5 F LIG 1 -8.417 4.546 -2.349 1.00 0.00 F ATOM 6 C LIG 1 -5.705 3.003 1.204 1.00 0.00 C ATOM 7 F LIG 1 -7.247 5.032 1.683 1.00 0.00 F ATOM 8 F LIG 1 -8.521 5.307 0.400 1.00 0.00 F ATOM 9 C LIG 1 -3.913 4.878 2.109 1.00 0.00 C ATOM 10 F LIG 1 -4.358 3.650 -0.024 1.00 0.00 F ATOM 11 F LIG 1 -6.198 1.346 0.214 1.00 0.00 F ATOM 12 C LIG 1 -1.306 5.673 2.286 1.00 0.00 C ATOM 13 F LIG 1 -3.429 3.111 0.668 1.00 0.00 F ATOM 14 F LIG 1 -2.358 3.855 1.570 1.00 0.00 F ATOM 15 C LIG 1 0.246 3.040 2.048 1.00 0.00 C ATOM 16 F LIG 1 -0.514 4.358 3.241 1.00 0.00 F ATOM 17 F LIG 1 -0.928 3.807 1.741 1.00 0.00 F ATOM 18 C LIG 1 1.925 3.706 2.014 1.00 0.00 C ATOM 19 F LIG 1 -0.226 2.548 0.094 1.00 0.00 F ATOM 20 F LIG 1 0.215 1.482 1.590 1.00 0.00 F ATOM 21 F LIG 1 -11.789 4.355 -2.598 1.00 0.00 F ATOM 22 F LIG 1 -11.552 4.133 -0.632 1.00 0.00 F ATOM 23 F LIG 1 2.299 2.385 2.438 1.00 0.00 F ATOM 24 F LIG 1 1.831 1.994 1.526 1.00 0.00 F ATOM 25 OM SCH 2 3.334 3.720 1.360 1.00 0.00 O ATOM 26 C SCH 2 5.273 2.985 0.897 1.00 0.00 C ATOM 27 C SCH 2 6.100 2.445 1.642 1.00 0.00 C ATOM 28 F SCH 2 4.528 2.997 1.631 1.00 0.00 F ATOM 29 F SCH 2 6.122 3.473 0.467 1.00 0.00 F ATOM 30 C SCH 2 7.274 1.746 2.026 1.00 0.00 C ATOM 31 OM SCH 2 5.454 2.160 2.446 1.00 0.00 O ATOM 32 F SCH 2 6.788 2.944 0.993 1.00 0.00 F ATOM 33 F SCH 2 7.031 1.025 2.779 1.00 0.00 F ATOM 34 F SCH 2 8.010 2.431 2.393 1.00 0.00 F ATOM 35 F SCH 2 7.678 1.241 1.173 1.00 0.00 F ATOM 36 C SCH 2 5.042 1.305 2.243 1.00 0.00 C ATOM 37 C SCH 2 5.168 0.043 2.583 1.00 0.00 C ATOM 38 F SCH 2 4.938 1.296 1.178 1.00 0.00 F ATOM 39 F SCH 2 4.377 1.446 3.070 1.00 0.00 F ATOM 40 S SCH 2 5.516 -1.463 2.733 1.00 0.00 S ATOM 41 F SCH 2 4.304 0.015 3.213 1.00 0.00 F ATOM 42 F SCH 2 6.073 0.088 2.014 1.00 0.00 F ATOM 43 O SCH 2 4.555 -2.079 3.473 1.00 0.00 O ATOM 44 H SCH 2 4.772 -3.020 3.567 1.00 0.00 H ATOM 45 O SCH 2 6.692 -1.508 1.977 1.00 0.00 O ATOM 46 O SCH 2 6.001 -2.846 2.762 1.00 0.00 O CONECT12 21 22 CONECT21345 CONECT2 CONECT32678 CONECT3 CONECT42 CONECT52 CONECT639 10 11 CONECT6 CONECT73 CONECT83 CONECT96 12 13 14 CONECT9 CONECT 106 CONECT 116 CONECT 129 15 16 17 CONECT 12 CONECT 139
Re: [gmx-users] ionomer topolgy
On 9/27/13 3:17 PM, Ehsan Sadeghi wrote: Many thanks Justin. Here is my .pdb file: ATOM 1 C LIG 1 -10.450 5.214 -1.717 1.00 0.00 C ATOM 2 C LIG 1 -8.424 5.477 -1.030 1.00 0.00 C ATOM 3 C LIG 1 -6.603 5.864 -0.166 1.00 0.00 C ATOM 4 F LIG 1 -6.651 6.230 -1.691 1.00 0.00 F ATOM 5 F LIG 1 -8.417 4.546 -2.349 1.00 0.00 F ATOM 6 C LIG 1 -5.705 3.003 1.204 1.00 0.00 C ATOM 7 F LIG 1 -7.247 5.032 1.683 1.00 0.00 F ATOM 8 F LIG 1 -8.521 5.307 0.400 1.00 0.00 F ATOM 9 C LIG 1 -3.913 4.878 2.109 1.00 0.00 C ATOM 10 F LIG 1 -4.358 3.650 -0.024 1.00 0.00 F ATOM 11 F LIG 1 -6.198 1.346 0.214 1.00 0.00 F ATOM 12 C LIG 1 -1.306 5.673 2.286 1.00 0.00 C ATOM 13 F LIG 1 -3.429 3.111 0.668 1.00 0.00 F ATOM 14 F LIG 1 -2.358 3.855 1.570 1.00 0.00 F ATOM 15 C LIG 1 0.246 3.040 2.048 1.00 0.00 C ATOM 16 F LIG 1 -0.514 4.358 3.241 1.00 0.00 F ATOM 17 F LIG 1 -0.928 3.807 1.741 1.00 0.00 F ATOM 18 C LIG 1 1.925 3.706 2.014 1.00 0.00 C ATOM 19 F LIG 1 -0.226 2.548 0.094 1.00 0.00 F ATOM 20 F LIG 1 0.215 1.482 1.590 1.00 0.00 F ATOM 21 F LIG 1 -11.789 4.355 -2.598 1.00 0.00 F ATOM 22 F LIG 1 -11.552 4.133 -0.632 1.00 0.00 F ATOM 23 F LIG 1 2.299 2.385 2.438 1.00 0.00 F ATOM 24 F LIG 1 1.831 1.994 1.526 1.00 0.00 F ATOM 25 OM SCH 2 3.334 3.720 1.360 1.00 0.00 O ATOM 26 C SCH 2 5.273 2.985 0.897 1.00 0.00 C ATOM 27 C SCH 2 6.100 2.445 1.642 1.00 0.00 C ATOM 28 F SCH 2 4.528 2.997 1.631 1.00 0.00 F ATOM 29 F SCH 2 6.122 3.473 0.467 1.00 0.00 F ATOM 30 C SCH 2 7.274 1.746 2.026 1.00 0.00 C ATOM 31 OM SCH 2 5.454 2.160 2.446 1.00 0.00 O ATOM 32 F SCH 2 6.788 2.944 0.993 1.00 0.00 F ATOM 33 F SCH 2 7.031 1.025 2.779 1.00 0.00 F ATOM 34 F SCH 2 8.010 2.431 2.393 1.00 0.00 F ATOM 35 F SCH 2 7.678 1.241 1.173 1.00 0.00 F ATOM 36 C SCH 2 5.042 1.305 2.243 1.00 0.00 C ATOM 37 C SCH 2 5.168 0.043 2.583 1.00 0.00 C ATOM 38 F SCH 2 4.938 1.296 1.178 1.00 0.00 F ATOM 39 F SCH 2 4.377 1.446 3.070 1.00 0.00 F ATOM 40 S SCH 2 5.516 -1.463 2.733 1.00 0.00 S ATOM 41 F SCH 2 4.304 0.015 3.213 1.00 0.00 F ATOM 42 F SCH 2 6.073 0.088 2.014 1.00 0.00 F ATOM 43 O SCH 2 4.555 -2.079 3.473 1.00 0.00 O ATOM 44 H SCH 2 4.772 -3.020 3.567 1.00 0.00 H ATOM 45 O SCH 2 6.692 -1.508 1.977 1.00 0.00 O ATOM 46 O SCH 2 6.001 -2.846 2.762 1.00 0.00 O CONECT12 21 22 CONECT21345 CONECT2 CONECT32678 CONECT3 CONECT42 CONECT52 CONECT639 10 11 CONECT6 CONECT73 CONECT83 CONECT96 12 13 14 CONECT9 CONECT 106 CONECT 116 CONECT 129 15 16 17 CONECT 12 CONECT 139 CONECT 149 CONECT 15 12 18 19 20 CONECT 15 CONECT 16 12 CONECT 17 12 CONECT 18 15 23 24 25 CONECT 18 CONECT 19 15 CONECT 20 15 CONECT 211 CONECT 221 CONECT 23 18 CONECT 24 18 CONECT 25 18 26 CONECT 26 25 27 28 29 CONECT 26 CONECT 27 26 30 31 32 CONECT 27 CONECT 28 26 CONECT 29 26 CONECT 30 27 33 34 35 CONECT 30 CONECT 31 27 36 CONECT 32 27 CONECT 33 30 CONECT 34 30 CONECT 35 30 CONECT 36 31 37 38 39 CONECT 36 CONECT 37 36 40 41 42 CONECT 37 CONECT 38 36 CONECT 39 36 CONECT 40 37 43 45 46 CONECT 40 CONECT 41 37 CONECT 42 37 CONECT 43 40 44 CONECT 44 43 CONECT 45 40 CONECT 46 40 MASTER00000000 460 460 END
Re: [gmx-users] ionomer topolgy
Hi, I just added this to the existing .rtp file in gromos [ LIG ] [ atoms ] C C 0.000 0 F F 0.000 0 [ SCH ] [ atoms ] OOM 0.000 0 C C 0.000 0 O O 0.000 0 F F 0.000 0 S S 0.000 0 H H 0.000 0 I also added LIG and SCH to the residuetypes.dat Kind regards, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, September 27, 2013 12:29:38 PM Subject: Re: [gmx-users] ionomer topolgy On 9/27/13 3:17 PM, Ehsan Sadeghi wrote: Many thanks Justin. Here is my .pdb file: ATOM 1 C LIG 1 -10.450 5.214 -1.717 1.00 0.00 C ATOM 2 C LIG 1 -8.424 5.477 -1.030 1.00 0.00 C ATOM 3 C LIG 1 -6.603 5.864 -0.166 1.00 0.00 C ATOM 4 F LIG 1 -6.651 6.230 -1.691 1.00 0.00 F ATOM 5 F LIG 1 -8.417 4.546 -2.349 1.00 0.00 F ATOM 6 C LIG 1 -5.705 3.003 1.204 1.00 0.00 C ATOM 7 F LIG 1 -7.247 5.032 1.683 1.00 0.00 F ATOM 8 F LIG 1 -8.521 5.307 0.400 1.00 0.00 F ATOM 9 C LIG 1 -3.913 4.878 2.109 1.00 0.00 C ATOM 10 F LIG 1 -4.358 3.650 -0.024 1.00 0.00 F ATOM 11 F LIG 1 -6.198 1.346 0.214 1.00 0.00 F ATOM 12 C LIG 1 -1.306 5.673 2.286 1.00 0.00 C ATOM 13 F LIG 1 -3.429 3.111 0.668 1.00 0.00 F ATOM 14 F LIG 1 -2.358 3.855 1.570 1.00 0.00 F ATOM 15 C LIG 1 0.246 3.040 2.048 1.00 0.00 C ATOM 16 F LIG 1 -0.514 4.358 3.241 1.00 0.00 F ATOM 17 F LIG 1 -0.928 3.807 1.741 1.00 0.00 F ATOM 18 C LIG 1 1.925 3.706 2.014 1.00 0.00 C ATOM 19 F LIG 1 -0.226 2.548 0.094 1.00 0.00 F ATOM 20 F LIG 1 0.215 1.482 1.590 1.00 0.00 F ATOM 21 F LIG 1 -11.789 4.355 -2.598 1.00 0.00 F ATOM 22 F LIG 1 -11.552 4.133 -0.632 1.00 0.00 F ATOM 23 F LIG 1 2.299 2.385 2.438 1.00 0.00 F ATOM 24 F LIG 1 1.831 1.994 1.526 1.00 0.00 F ATOM 25 OM SCH 2 3.334 3.720 1.360 1.00 0.00 O ATOM 26 C SCH 2 5.273 2.985 0.897 1.00 0.00 C ATOM 27 C SCH 2 6.100 2.445 1.642 1.00 0.00 C ATOM 28 F SCH 2 4.528 2.997 1.631 1.00 0.00 F ATOM 29 F SCH 2 6.122 3.473 0.467 1.00 0.00 F ATOM 30 C SCH 2 7.274 1.746 2.026 1.00 0.00 C ATOM 31 OM SCH 2 5.454 2.160 2.446 1.00 0.00 O ATOM 32 F SCH 2 6.788 2.944 0.993 1.00 0.00 F ATOM 33 F SCH 2 7.031 1.025 2.779 1.00 0.00 F ATOM 34 F SCH 2 8.010 2.431 2.393 1.00 0.00 F ATOM 35 F SCH 2 7.678 1.241 1.173 1.00 0.00 F ATOM 36 C SCH 2 5.042 1.305 2.243 1.00 0.00 C ATOM 37 C SCH 2 5.168 0.043 2.583 1.00 0.00 C ATOM 38 F SCH 2 4.938 1.296 1.178 1.00 0.00 F ATOM 39 F SCH 2 4.377 1.446 3.070 1.00 0.00 F ATOM 40 S SCH 2 5.516 -1.463 2.733 1.00 0.00 S ATOM 41 F SCH 2 4.304 0.015 3.213 1.00 0.00 F ATOM 42 F SCH 2 6.073 0.088 2.014 1.00 0.00 F ATOM 43 O SCH 2 4.555 -2.079 3.473 1.00 0.00 O ATOM 44 H SCH 2 4.772 -3.020 3.567 1.00 0.00 H ATOM 45 O SCH 2 6.692 -1.508 1.977 1.00 0.00 O ATOM 46 O SCH 2 6.001 -2.846 2.762 1.00 0.00 O CONECT12 21 22 CONECT21345 CONECT2 CONECT32678 CONECT3 CONECT42 CONECT52 CONECT639 10 11 CONECT6 CONECT73 CONECT83 CONECT96 12 13 14 CONECT9 CONECT 106 CONECT 116 CONECT 129 15 16 17 CONECT 12 CONECT 139 CONECT 149 CONECT 15 12 18 19 20 CONECT 15 CONECT 16 12 CONECT 17 12 CONECT 18 15 23 24 25 CONECT 18 CONECT 19 15 CONECT 20 15 CONECT 211 CONECT 221 CONECT 23 18 CONECT
Re: [gmx-users] ionomer topolgy
On 9/27/13 4:18 PM, Ehsan Sadeghi wrote: Hi, I just added this to the existing .rtp file in gromos [ LIG ] [ atoms ] C C 0.000 0 F F 0.000 0 [ SCH ] [ atoms ] OOM 0.000 0 C C 0.000 0 O O 0.000 0 F F 0.000 0 S S 0.000 0 H H 0.000 0 I also added LIG and SCH to the residuetypes.dat Your definition of LIG in the .rtp entry does not come anywhere close to matching what is in the .pdb file. If, in fact, each residue only has two atoms (I don't see how that's chemically possible), then your residue numbers have to follow suit. As it stands now, pdb2gmx is trying to find a 24-atom LIG residue and a 22-atom SCH. Neither of these is true, per the .rtp. -Justin Kind regards, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, September 27, 2013 12:29:38 PM Subject: Re: [gmx-users] ionomer topolgy On 9/27/13 3:17 PM, Ehsan Sadeghi wrote: Many thanks Justin. Here is my .pdb file: ATOM 1 C LIG 1 -10.450 5.214 -1.717 1.00 0.00 C ATOM 2 C LIG 1 -8.424 5.477 -1.030 1.00 0.00 C ATOM 3 C LIG 1 -6.603 5.864 -0.166 1.00 0.00 C ATOM 4 F LIG 1 -6.651 6.230 -1.691 1.00 0.00 F ATOM 5 F LIG 1 -8.417 4.546 -2.349 1.00 0.00 F ATOM 6 C LIG 1 -5.705 3.003 1.204 1.00 0.00 C ATOM 7 F LIG 1 -7.247 5.032 1.683 1.00 0.00 F ATOM 8 F LIG 1 -8.521 5.307 0.400 1.00 0.00 F ATOM 9 C LIG 1 -3.913 4.878 2.109 1.00 0.00 C ATOM 10 F LIG 1 -4.358 3.650 -0.024 1.00 0.00 F ATOM 11 F LIG 1 -6.198 1.346 0.214 1.00 0.00 F ATOM 12 C LIG 1 -1.306 5.673 2.286 1.00 0.00 C ATOM 13 F LIG 1 -3.429 3.111 0.668 1.00 0.00 F ATOM 14 F LIG 1 -2.358 3.855 1.570 1.00 0.00 F ATOM 15 C LIG 1 0.246 3.040 2.048 1.00 0.00 C ATOM 16 F LIG 1 -0.514 4.358 3.241 1.00 0.00 F ATOM 17 F LIG 1 -0.928 3.807 1.741 1.00 0.00 F ATOM 18 C LIG 1 1.925 3.706 2.014 1.00 0.00 C ATOM 19 F LIG 1 -0.226 2.548 0.094 1.00 0.00 F ATOM 20 F LIG 1 0.215 1.482 1.590 1.00 0.00 F ATOM 21 F LIG 1 -11.789 4.355 -2.598 1.00 0.00 F ATOM 22 F LIG 1 -11.552 4.133 -0.632 1.00 0.00 F ATOM 23 F LIG 1 2.299 2.385 2.438 1.00 0.00 F ATOM 24 F LIG 1 1.831 1.994 1.526 1.00 0.00 F ATOM 25 OM SCH 2 3.334 3.720 1.360 1.00 0.00 O ATOM 26 C SCH 2 5.273 2.985 0.897 1.00 0.00 C ATOM 27 C SCH 2 6.100 2.445 1.642 1.00 0.00 C ATOM 28 F SCH 2 4.528 2.997 1.631 1.00 0.00 F ATOM 29 F SCH 2 6.122 3.473 0.467 1.00 0.00 F ATOM 30 C SCH 2 7.274 1.746 2.026 1.00 0.00 C ATOM 31 OM SCH 2 5.454 2.160 2.446 1.00 0.00 O ATOM 32 F SCH 2 6.788 2.944 0.993 1.00 0.00 F ATOM 33 F SCH 2 7.031 1.025 2.779 1.00 0.00 F ATOM 34 F SCH 2 8.010 2.431 2.393 1.00 0.00 F ATOM 35 F SCH 2 7.678 1.241 1.173 1.00 0.00 F ATOM 36 C SCH 2 5.042 1.305 2.243 1.00 0.00 C ATOM 37 C SCH 2 5.168 0.043 2.583 1.00 0.00 C ATOM 38 F SCH 2 4.938 1.296 1.178 1.00 0.00 F ATOM 39 F SCH 2 4.377 1.446 3.070 1.00 0.00 F ATOM 40 S SCH 2 5.516 -1.463 2.733 1.00 0.00 S ATOM 41 F SCH 2 4.304 0.015 3.213 1.00 0.00 F ATOM 42 F SCH 2 6.073 0.088 2.014 1.00 0.00 F ATOM 43 O SCH 2 4.555 -2.079 3.473 1.00 0.00 O ATOM 44 H SCH 2 4.772 -3.020 3.567 1.00 0.00 H ATOM 45 O SCH 2 6.692 -1.508 1.977 1.00 0.00 O ATOM 46 O SCH 2 6.001 -2.846 2.762 1.00 0.00 O CONECT12 21 22 CONECT21345 CONECT2 CONECT32678 CONECT3 CONECT42 CONECT52 CONECT639 10 11 CONECT6 CONECT73 CONECT83
[gmx-users] RE: Membrane simulation with OPLS ff.
Thanks Chris. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Christopher Neale Sent: Thursday, September 26, 2013 7:47 PM To: gmx-users@gromacs.org Subject: [gmx-users] Membrane simulation with OPLS ff. Dear Karthi: As far as I am aware, there is no OPLSAA lipid force field. I have used Berger lipids with OPLSAA protein ( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but that is mixing a UA lipid with an AA protein so be aware of possible problems arising out of that. Charmm has proteins and lipids, but charmm lipids require charmm tip3p water (or at least tip4p or spc, certainly not regular tip3p) and are thus slower to simulate in gromacs. I'm more recently using the Slipids (stockholm lipids) and Amber99SB-ILDN protein forcefield. Chris. -- original message -- Is OPLSAA forcefield data already available for POPC membranes. I am interested in simulation of proteins in POPC membrane. Thank you. Best Regards Karthi. -- 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 -- 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
Re: [gmx-users] ionomer topolgy
Thanks Justin. I try to modify my file based on your comments. - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, September 27, 2013 1:24:44 PM Subject: Re: [gmx-users] ionomer topolgy On 9/27/13 4:18 PM, Ehsan Sadeghi wrote: Hi, I just added this to the existing .rtp file in gromos [ LIG ] [ atoms ] C C 0.000 0 F F 0.000 0 [ SCH ] [ atoms ] OOM 0.000 0 C C 0.000 0 O O 0.000 0 F F 0.000 0 S S 0.000 0 H H 0.000 0 I also added LIG and SCH to the residuetypes.dat Your definition of LIG in the .rtp entry does not come anywhere close to matching what is in the .pdb file. If, in fact, each residue only has two atoms (I don't see how that's chemically possible), then your residue numbers have to follow suit. As it stands now, pdb2gmx is trying to find a 24-atom LIG residue and a 22-atom SCH. Neither of these is true, per the .rtp. -Justin Kind regards, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, September 27, 2013 12:29:38 PM Subject: Re: [gmx-users] ionomer topolgy On 9/27/13 3:17 PM, Ehsan Sadeghi wrote: Many thanks Justin. Here is my .pdb file: ATOM 1 C LIG 1 -10.450 5.214 -1.717 1.00 0.00 C ATOM 2 C LIG 1 -8.424 5.477 -1.030 1.00 0.00 C ATOM 3 C LIG 1 -6.603 5.864 -0.166 1.00 0.00 C ATOM 4 F LIG 1 -6.651 6.230 -1.691 1.00 0.00 F ATOM 5 F LIG 1 -8.417 4.546 -2.349 1.00 0.00 F ATOM 6 C LIG 1 -5.705 3.003 1.204 1.00 0.00 C ATOM 7 F LIG 1 -7.247 5.032 1.683 1.00 0.00 F ATOM 8 F LIG 1 -8.521 5.307 0.400 1.00 0.00 F ATOM 9 C LIG 1 -3.913 4.878 2.109 1.00 0.00 C ATOM 10 F LIG 1 -4.358 3.650 -0.024 1.00 0.00 F ATOM 11 F LIG 1 -6.198 1.346 0.214 1.00 0.00 F ATOM 12 C LIG 1 -1.306 5.673 2.286 1.00 0.00 C ATOM 13 F LIG 1 -3.429 3.111 0.668 1.00 0.00 F ATOM 14 F LIG 1 -2.358 3.855 1.570 1.00 0.00 F ATOM 15 C LIG 1 0.246 3.040 2.048 1.00 0.00 C ATOM 16 F LIG 1 -0.514 4.358 3.241 1.00 0.00 F ATOM 17 F LIG 1 -0.928 3.807 1.741 1.00 0.00 F ATOM 18 C LIG 1 1.925 3.706 2.014 1.00 0.00 C ATOM 19 F LIG 1 -0.226 2.548 0.094 1.00 0.00 F ATOM 20 F LIG 1 0.215 1.482 1.590 1.00 0.00 F ATOM 21 F LIG 1 -11.789 4.355 -2.598 1.00 0.00 F ATOM 22 F LIG 1 -11.552 4.133 -0.632 1.00 0.00 F ATOM 23 F LIG 1 2.299 2.385 2.438 1.00 0.00 F ATOM 24 F LIG 1 1.831 1.994 1.526 1.00 0.00 F ATOM 25 OM SCH 2 3.334 3.720 1.360 1.00 0.00 O ATOM 26 C SCH 2 5.273 2.985 0.897 1.00 0.00 C ATOM 27 C SCH 2 6.100 2.445 1.642 1.00 0.00 C ATOM 28 F SCH 2 4.528 2.997 1.631 1.00 0.00 F ATOM 29 F SCH 2 6.122 3.473 0.467 1.00 0.00 F ATOM 30 C SCH 2 7.274 1.746 2.026 1.00 0.00 C ATOM 31 OM SCH 2 5.454 2.160 2.446 1.00 0.00 O ATOM 32 F SCH 2 6.788 2.944 0.993 1.00 0.00 F ATOM 33 F SCH 2 7.031 1.025 2.779 1.00 0.00 F ATOM 34 F SCH 2 8.010 2.431 2.393 1.00 0.00 F ATOM 35 F SCH 2 7.678 1.241 1.173 1.00 0.00 F ATOM 36 C SCH 2 5.042 1.305 2.243 1.00 0.00 C ATOM 37 C SCH 2 5.168 0.043 2.583 1.00 0.00 C ATOM 38 F SCH 2 4.938 1.296 1.178 1.00 0.00 F ATOM 39 F SCH 2 4.377 1.446 3.070 1.00 0.00 F ATOM 40 S SCH 2 5.516 -1.463 2.733 1.00 0.00 S ATOM 41 F SCH 2 4.304 0.015 3.213 1.00 0.00 F ATOM 42 F SCH 2 6.073 0.088 2.014 1.00 0.00 F ATOM 43 O SCH 2 4.555 -2.079 3.473 1.00 0.00 O ATOM 44 H SCH 2 4.772
RE: [gmx-users] Membrane simulation with OPLS ff.
Thanks Justin. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: Thursday, September 26, 2013 7:51 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Membrane simulation with OPLS ff. On 9/26/13 10:47 PM, Christopher Neale wrote: Dear Karthi: As far as I am aware, there is no OPLSAA lipid force field. I have used Berger lipids with OPLSAA protein ( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but that is mixing a UA lipid with an AA protein so be aware of possible problems arising out of that. There are OPLS-compatible lipids, though they are UA, but specifically designed to be used with OPLS-AA: dx.doi.org/10.1021/ct900086b I have not seen these parameters used very widely, though. Charmm has proteins and lipids, but charmm lipids require charmm tip3p water (or at least tip4p or spc, certainly not regular tip3p) and are thus slower to simulate in gromacs. I'm more recently using the Slipids (stockholm lipids) and Amber99SB-ILDN protein forcefield. Solid choices. -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 -- 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
Re: [gmx-users] ionomer topolgy
Hello, I revised my pdb and rtp files. I still receive similar error message. Here are the new files: .pdb: ATOM 1 C1LIG 1 -10.450 5.214 -1.717 1.00 0.00 C ATOM 2 C2LIG 1 -8.424 5.477 -1.030 1.00 0.00 C ATOM 3 C3LIG 1 -6.603 5.864 -0.166 1.00 0.00 C ATOM 4 F1LIG 1 -6.651 6.230 -1.691 1.00 0.00 F ATOM 5 F2LIG 1 -8.417 4.546 -2.349 1.00 0.00 F ATOM 6 C4LIG 1 -5.705 3.003 1.204 1.00 0.00 C ATOM 7 F3LIG 1 -7.247 5.032 1.683 1.00 0.00 F ATOM 8 F4LIG 1 -8.521 5.307 0.400 1.00 0.00 F ATOM 9 C5LIG 1 -3.913 4.878 2.109 1.00 0.00 C ATOM 10 F5LIG 1 -4.358 3.650 -0.024 1.00 0.00 F ATOM 11 F6LIG 1 -6.198 1.346 0.214 1.00 0.00 F ATOM 12 C6LIG 1 -1.306 5.673 2.286 1.00 0.00 C ATOM 13 F7LIG 1 -3.429 3.111 0.668 1.00 0.00 F ATOM 14 F8LIG 1 -2.358 3.855 1.570 1.00 0.00 F ATOM 15 C7LIG 1 0.246 3.040 2.048 1.00 0.00 C ATOM 16 F9LIG 1 -0.514 4.358 3.241 1.00 0.00 F ATOM 17 F10 LIG 1 -0.928 3.807 1.741 1.00 0.00 F ATOM 18 C8LIG 1 1.925 3.706 2.014 1.00 0.00 C ATOM 19 F11 LIG 1 -0.226 2.548 0.094 1.00 0.00 F ATOM 20 F12 LIG 1 0.215 1.482 1.590 1.00 0.00 F ATOM 21 F13 LIG 1 -11.789 4.355 -2.598 1.00 0.00 F ATOM 22 F14 LIG 1 -11.552 4.133 -0.632 1.00 0.00 F ATOM 23 F15 LIG 1 2.299 2.385 2.438 1.00 0.00 F ATOM 24 F16 LIG 1 1.831 1.994 1.526 1.00 0.00 F ATOM 25 O1SCH 2 3.334 3.720 1.360 1.00 0.00 O ATOM 26 C1SCH 2 5.273 2.985 0.897 1.00 0.00 C ATOM 27 C2SCH 2 6.100 2.445 1.642 1.00 0.00 C ATOM 28 F1SCH 2 4.528 2.997 1.631 1.00 0.00 F ATOM 29 F2SCH 2 6.122 3.473 0.467 1.00 0.00 F ATOM 30 C3SCH 2 7.274 1.746 2.026 1.00 0.00 C ATOM 31 O2SCH 2 5.454 2.160 2.446 1.00 0.00 O ATOM 32 F3SCH 2 6.788 2.944 0.993 1.00 0.00 F ATOM 33 F4SCH 2 7.031 1.025 2.779 1.00 0.00 F ATOM 34 F5SCH 2 8.010 2.431 2.393 1.00 0.00 F ATOM 35 F6SCH 2 7.678 1.241 1.173 1.00 0.00 F ATOM 36 C4SCH 2 5.042 1.305 2.243 1.00 0.00 C ATOM 37 C5SCH 2 5.168 0.043 2.583 1.00 0.00 C ATOM 38 F7SCH 2 4.938 1.296 1.178 1.00 0.00 F ATOM 39 F8SCH 2 4.377 1.446 3.070 1.00 0.00 F ATOM 40 S SCH 2 5.516 -1.463 2.733 1.00 0.00 S ATOM 41 F9SCH 2 4.304 0.015 3.213 1.00 0.00 F ATOM 42 F10 SCH 2 6.073 0.088 2.014 1.00 0.00 F ATOM 43 O3SCH 2 4.555 -2.079 3.473 1.00 0.00 O ATOM 44 H SCH 2 4.772 -3.020 3.567 1.00 0.00 H ATOM 45 O4SCH 2 6.692 -1.508 1.977 1.00 0.00 O ATOM 46 O5SCH 2 6.001 -2.846 2.762 1.00 0.00 O -- .rtp [ LIG ] [ atoms ] C1 C 0.000 0 C2 C 0.000 0 C3 C 0.000 0 F1 F 0.000 0 F2 F 0.000 0 C4 C 0.000 0 F3 F 0.000 0 F4 F 0.000 0 C5 C 0.000 0 F5 F 0.000 0 F6 F 0.000 0 C6 C 0.000 0 F7 F 0.000 0 F8 F 0.000 0 C7 C 0.000 0 F9 F 0.000 0 F10F 0.000 0 C8 C 0.000 0 F11F 0.000 0 F12F 0.000 0 F13F 0.000 0 F14F 0.000 0 F15F 0.000 0 F16F 0.000 0 [ SCH ] [ atoms ] O1OM 0.000 0 C1 C 0.000 0 C2 C 0.000 0 F1 F 0.000 0 F2 F 0.000 0 C3 C 0.000 0 O2OM 0.000 0 F3 F 0.000 0 F4 F 0.000 0 F5 F
Re: [gmx-users] ionomer topolgy
On 9/27/13 5:53 PM, Ehsan Sadeghi wrote: Hello, I revised my pdb and rtp files. I still receive similar error message. Whatever modifications you're making probably aren't being done in the right files. You haven't yet responded to my question about which force field you're using and whether you're making modifications in the working directory or in $GMXLIB. Exact screen output from pdb2gmx would be very useful here. Please post the exact command and all screen output, including your selections and the error message. -Justin Here are the new files: .pdb: ATOM 1 C1LIG 1 -10.450 5.214 -1.717 1.00 0.00 C ATOM 2 C2LIG 1 -8.424 5.477 -1.030 1.00 0.00 C ATOM 3 C3LIG 1 -6.603 5.864 -0.166 1.00 0.00 C ATOM 4 F1LIG 1 -6.651 6.230 -1.691 1.00 0.00 F ATOM 5 F2LIG 1 -8.417 4.546 -2.349 1.00 0.00 F ATOM 6 C4LIG 1 -5.705 3.003 1.204 1.00 0.00 C ATOM 7 F3LIG 1 -7.247 5.032 1.683 1.00 0.00 F ATOM 8 F4LIG 1 -8.521 5.307 0.400 1.00 0.00 F ATOM 9 C5LIG 1 -3.913 4.878 2.109 1.00 0.00 C ATOM 10 F5LIG 1 -4.358 3.650 -0.024 1.00 0.00 F ATOM 11 F6LIG 1 -6.198 1.346 0.214 1.00 0.00 F ATOM 12 C6LIG 1 -1.306 5.673 2.286 1.00 0.00 C ATOM 13 F7LIG 1 -3.429 3.111 0.668 1.00 0.00 F ATOM 14 F8LIG 1 -2.358 3.855 1.570 1.00 0.00 F ATOM 15 C7LIG 1 0.246 3.040 2.048 1.00 0.00 C ATOM 16 F9LIG 1 -0.514 4.358 3.241 1.00 0.00 F ATOM 17 F10 LIG 1 -0.928 3.807 1.741 1.00 0.00 F ATOM 18 C8LIG 1 1.925 3.706 2.014 1.00 0.00 C ATOM 19 F11 LIG 1 -0.226 2.548 0.094 1.00 0.00 F ATOM 20 F12 LIG 1 0.215 1.482 1.590 1.00 0.00 F ATOM 21 F13 LIG 1 -11.789 4.355 -2.598 1.00 0.00 F ATOM 22 F14 LIG 1 -11.552 4.133 -0.632 1.00 0.00 F ATOM 23 F15 LIG 1 2.299 2.385 2.438 1.00 0.00 F ATOM 24 F16 LIG 1 1.831 1.994 1.526 1.00 0.00 F ATOM 25 O1SCH 2 3.334 3.720 1.360 1.00 0.00 O ATOM 26 C1SCH 2 5.273 2.985 0.897 1.00 0.00 C ATOM 27 C2SCH 2 6.100 2.445 1.642 1.00 0.00 C ATOM 28 F1SCH 2 4.528 2.997 1.631 1.00 0.00 F ATOM 29 F2SCH 2 6.122 3.473 0.467 1.00 0.00 F ATOM 30 C3SCH 2 7.274 1.746 2.026 1.00 0.00 C ATOM 31 O2SCH 2 5.454 2.160 2.446 1.00 0.00 O ATOM 32 F3SCH 2 6.788 2.944 0.993 1.00 0.00 F ATOM 33 F4SCH 2 7.031 1.025 2.779 1.00 0.00 F ATOM 34 F5SCH 2 8.010 2.431 2.393 1.00 0.00 F ATOM 35 F6SCH 2 7.678 1.241 1.173 1.00 0.00 F ATOM 36 C4SCH 2 5.042 1.305 2.243 1.00 0.00 C ATOM 37 C5SCH 2 5.168 0.043 2.583 1.00 0.00 C ATOM 38 F7SCH 2 4.938 1.296 1.178 1.00 0.00 F ATOM 39 F8SCH 2 4.377 1.446 3.070 1.00 0.00 F ATOM 40 S SCH 2 5.516 -1.463 2.733 1.00 0.00 S ATOM 41 F9SCH 2 4.304 0.015 3.213 1.00 0.00 F ATOM 42 F10 SCH 2 6.073 0.088 2.014 1.00 0.00 F ATOM 43 O3SCH 2 4.555 -2.079 3.473 1.00 0.00 O ATOM 44 H SCH 2 4.772 -3.020 3.567 1.00 0.00 H ATOM 45 O4SCH 2 6.692 -1.508 1.977 1.00 0.00 O ATOM 46 O5SCH 2 6.001 -2.846 2.762 1.00 0.00 O -- .rtp [ LIG ] [ atoms ] C1 C 0.000 0 C2 C 0.000 0 C3 C 0.000 0 F1 F 0.000 0 F2 F 0.000 0 C4 C 0.000 0 F3 F 0.000 0 F4 F 0.000 0 C5 C 0.000 0 F5 F 0.000 0 F6 F 0.000 0 C6 C 0.000 0 F7 F 0.000 0 F8 F 0.000 0 C7 C 0.000 0 F9 F 0.000 0 F10F 0.000 0 C8 C 0.000 0 F11F 0.000 0 F12F 0.000 0 F13F 0.000 0 F14F
Re: [gmx-users] ionomer topolgy
Thanks for your prompt response. I made the modifications on the aminoacids.rtp file in Gromacs/gromacs-4.6.3/share/top/gromos53a6.ff. I did not modify any force field. I thought I still can use the default force field in gromos; isn't it right? Here is the output from pdb2gmx. Thank you for your consideration. --- Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b Reading nafion3.pdb... WARNING: all CONECT records are ignored Read 46 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 2 chains and 0 blocks of water and 0 residues with 46 atoms chain #res #atoms 1 'G' 1 24 2 'H' 1 22 WARNING: there were 1 atoms with zero occupancy and 45 atoms with occupancy unequal to one (out of 46 atoms). Check your pdb file. Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/atomtypes.atp Atomtype 1 Reading residue database... (gromos53a6) Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Residue 108 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.36# Processing chain 1 'G' (24 atoms, 1 residues) Warning: Starting residue LI0 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.6.3 Source code file: /home/ehssad/Downloads/Gromacs/gromacs-4.6.3/src/kernel/resall.c, line: 642 Fatal error: Residue 'LI' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Thanks, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, September 27, 2013 3:06:05 PM Subject: Re: [gmx-users] ionomer topolgy On 9/27/13 5:53 PM, Ehsan Sadeghi wrote: Hello, I revised my pdb and rtp files. I still receive similar error message. Whatever modifications you're making probably aren't being done in the right files. You haven't yet responded to my question about which force field you're using and whether you're making modifications in the working directory or in $GMXLIB. Exact screen output from pdb2gmx would be very useful here. Please post the exact command and all screen output, including your selections and the error message. -Justin Here are the new files: .pdb: ATOM 1 C1LIG 1 -10.450 5.214 -1.717 1.00 0.00 C ATOM 2 C2LIG 1 -8.424 5.477 -1.030 1.00 0.00 C ATOM 3 C3LIG 1 -6.603 5.864 -0.166 1.00 0.00 C ATOM 4 F1LIG 1 -6.651 6.230 -1.691 1.00 0.00 F ATOM 5 F2LIG 1 -8.417 4.546 -2.349 1.00 0.00 F ATOM 6 C4LIG 1 -5.705 3.003 1.204 1.00 0.00 C ATOM 7 F3LIG 1 -7.247 5.032 1.683 1.00 0.00 F ATOM 8 F4LIG 1 -8.521 5.307 0.400 1.00 0.00 F ATOM 9 C5LIG 1 -3.913 4.878 2.109 1.00 0.00 C ATOM 10 F5LIG 1 -4.358 3.650 -0.024 1.00 0.00 F ATOM 11 F6LIG 1 -6.198 1.346 0.214 1.00 0.00 F ATOM 12 C6LIG 1 -1.306 5.673 2.286 1.00 0.00 C ATOM 13 F7LIG 1 -3.429 3.111 0.668 1.00 0.00 F ATOM 14 F8LIG 1 -2.358 3.855 1.570 1.00 0.00 F ATOM 15 C7LIG 1 0.246 3.040 2.048 1.00 0.00 C ATOM 16 F9LIG 1 -0.514 4.358 3.241 1.00 0.00 F ATOM 17 F10 LIG 1 -0.928 3.807 1.741 1.00 0.00 F ATOM 18 C8LIG 1 1.925 3.706 2.014 1.00 0.00 C ATOM 19 F11 LIG 1 -0.226 2.548 0.094 1.00 0.00 F ATOM 20 F12 LIG 1 0.215 1.482 1.590 1.00 0.00 F ATOM 21
Re: [gmx-users] ionomer topolgy
On 9/27/13 8:43 PM, Ehsan Sadeghi wrote: Thanks for your prompt response. I made the modifications on the aminoacids.rtp file in Gromacs/gromacs-4.6.3/share/top/gromos53a6.ff. I did not modify any force field. I thought I still can use the default force field in gromos; isn't it right? Yes you did; you modified the Gromos96 53A6 force field. There's nothing wrong with that; it's precisely what you wanted to do. Also note that there is no such thing as a default force field. Here is the output from pdb2gmx. Thank you for your consideration. --- Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b Reading nafion3.pdb... WARNING: all CONECT records are ignored Read 46 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 2 chains and 0 blocks of water and 0 residues with 46 atoms chain #res #atoms 1 'G' 1 24 2 'H' 1 22 WARNING: there were 1 atoms with zero occupancy and 45 atoms with occupancy unequal to one (out of 46 atoms). Check your pdb file. Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/atomtypes.atp Atomtype 1 Reading residue database... (gromos53a6) Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp Using default: not generating all possible dihedrals Using default: excluding 3 bonded neighbors Using default: generating 1,4 H--H interactions Using default: removing proper dihedrals found on the same bond as a proper dihedral Residue 108 Sorting it all out... Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.hdb Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb Opening force field file /usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.36# Processing chain 1 'G' (24 atoms, 1 residues) Warning: Starting residue LI0 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION 4.6.3 Source code file: /home/ehssad/Downloads/Gromacs/gromacs-4.6.3/src/kernel/resall.c, line: 642 Fatal error: Residue 'LI' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Now your problem is that the .pdb file is misformatted. Your residue name columns are shifted, such that pdb2gmx thinks LI is the residue and G is the chain identifier. PDB format is fixed; if you mess it up, the contents become unreadable (or severely misinterpreted). -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
Re: [gmx-users] OPLS/AA + TIP5P, anybody?
Dear Chris, Thank you for your reply. I defined a new virtual atomtype (type D) with LJ sigma 1.72A ( 2*0.7+1.72=3.12, which is sigma of the oxygen) and played a bit with epsilon till the new LJ repulsion was able to prevent the build up of a huge force on the oxygen while interacting with dimensionless charged hydrogens. Also, I copied the flexibility parameters from tip4p to see if it helps in minimization before I turn it into rigid water - it seems that it does. I was able to minimize the system with such water. Also, I minimized the system with tip4p and replaced it with tip5p with a script. I tried to minimize the system afterwards with true tip5p, which did not work. My question is, besides the correctness of water model, why do you think it is safe to remove the LJ on lone electron pairs in MD? Will it not collapse like in energy minimization? Best Regards, Grzegorz On 2013-09-27 05:58, Christopher Neale wrote: Dear Gigo: I've never used tip5p, but perhaps you could add some LJ terms to the opls_120 definition, do your minimization, then remove the fake LJ term on opls_120 and run your MD? If that doesn't work, then you might be able to minimize your system using FLEXIBLE tip3p water and then use a script to convert the tip3p into tip5p. I expect that you can set 0,0,0 coordinates for each of the tip5p dummy atoms and that they will get correctly positioned in your first mdrun step with tip5p. Chris. -- original message -- Dear Mark, Thank you for your reply. Unfortunately, TIP5P is completely rigid and the FLEXIBLE define will not change it. Any other ideas? Best, g On 2013-09-24 23:51, Mark Abraham wrote: You should be able to minimize with CG and TIP5P by eliminating constraints, by making the water use a flexible molecule, e.g. define = -DFLEXIBLE (or something). Check your water .itp file for how to do it. Mark -- 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
