[gmx-users] building up a long polymer chain
Dear experts,
For hexane molecule I used atom types
opls_157 12.01100 ; all-atom C: CH3 & CH2, alcohols
opls_158 12.01100 ; all-atom C: CH, alcohols
in residue file:
[ HEX ]
[ atoms ]
C1 opls_157-0.180 1
H11 opls_140 0.060 1
H12 opls_140 0.060 1
H13 opls_140 0.060 1
C2 opls_158-0.120 2
H21 opls_140 0.060 2
H22 opls_140 0.060 2
C3 opls_158-0.120 3
H31 opls_140 0.060 3
H32 opls_140 0.060 3
C4 opls_158-0.120 4
H41 opls_140 0.060 4
H42 opls_140 0.060 4
C5 opls_158-0.120 5
H51 opls_140 0.060 5
H52 opls_140 0.060 5
C6 opls_157-0.180 6
H61 opls_140 0.060 6
H62 opls_140 0.060 6
H63 opls_140 0.060 6
now that I am trying to create top file for polyethylene (PE) I doubt if I
pickec right atom types for hexane since I see in ffoplsaa.atp file:
opls_135 12.01100 ; alkane CH3
opls_136 12.01100 ; alkane CH2
for alkanes. Please let me know if I am right and I should use
opls_157 12.01100 ; all-atom C: CH3 & CH2, alcohols
opls_158 12.01100 ; all-atom C: CH, alcohols
for PE. or maybe this dies not affect the results since charges and mass are
the same..?!
Also: can opls_157 be used for both CH3 & CH2,on PE chain? what is the
suitable atom type for carbon atoms on PE chain?
2- I spent alot of time finding a solution for the following problem: I am
trying to build up a very long PE chain. to do this I am using the following
residues in rtp file:
; Polyethylene - this is an internal residue
[ Eth ]
[ atoms ]
C1opls_136-0.1201
H11 opls_140 0.0601
H12 opls_140 0.0601
C2opls_136-0.1202
H21 opls_140 0.0602
H22 opls_140 0.0602
[ bonds ]
C1-C2
C1H11
C1H12
C1C2
C2H21
C2H22
C2+C1
; Terminal PE residue ("beginning" of chain)
; designation arbitrary, C1 is -CH3
; designation arbitrary, C1 is -CH3
[ EthB ]
[ atoms ]
C1opls_135-0.1801
H11 opls_140 0.0601
H12 opls_140 0.0601
H13 opls_140 0.0601
C2opls_136-0.1202
H21 opls_140 0.0602
H22 opls_140 0.0602
[ bonds ]
C1H11
C1H12
C1H13
C1C2
C2H21
C2H22
C2+C
; Terminal PE residue ("end" of chain)
; designation arbitrary, C2 is -CH3
[ EthE ]
[ atoms ]
C1opls_136-0.1201
H11 opls_140 0.0601
H12 opls_140 0.0601
C2opls_135-0.1802
H21 opls_140 0.0602
H22 opls_140 0.0602
H23 opls_140 0.0602
[ bonds ]
C1-C
C1H11
C1H12
C1C2
C2H21
C2H22
C2H23
However, the software I am using(Ascalaph Desingner) to build up PE chain
lists atoms as shown below: (I changed the res names to Eth and EthB
myself). i.e. atoms have no numbering meaning that if I want to use the
above resudies in rtp file I will have to go thorough the whole structure
file(below) and do the numbering by myself (H to H11, H12, H21, H22...)and C
to C1 C2) which is a tedious work. when I want to generate a molecule of
4 Mw (about 1400 monomer units! or about 8000 atoms)
HETATM1 CB EthB1 2.739 2.554 -0.012 0.00 -0.39
C
HETATM2 H EthB1 2.736 3.644 -0.012 0.00 0.13
H
HETATM3 H EthB1 2.190 2.217 -0.893 0.00 0.13
H
HETATM4 H EthB1 2.190 2.217 0.868 0.00 0.13
H
HETATM5 C Eth 2 4.155 1.993 -0.012 0.00 -0.26
C
HETATM6 H Eth 2 4.696 2.362 -0.887 0.00 0.13
H
HETATM7 H Eth 2 4.696 2.362 0.862 0.00 0.13
H
HETATM8 C Eth 3 4.163 0.470 -0.012 0.00 -0.26
C
HETATM9 H Eth 3 3.623 0.101 0.862 0.00 0.13
H
HETATM 10 H Eth 3 3.623 0.101 -0.887 0.00 0.13
H
HETATM 11 C Eth 4 5.579 -0.091 -0.012 0.00 -0.26
C
HETATM 12 H Eth 4 6.119 0.278 -0.887 0.00 0.13
H
.
.
I numbered 350 atoms (60 monomer units) and simulation is working now.
56
1EthBC11 0.860 2.362 1.500
1EthB H112 0.860 2.471 1.500
1EthB H123 0.805 2.329 1.412
1EthB H134 0.805 2.329 1.588
1EthBC25 1.002 2.306 1.500
1EthB H216 1.056 2.343 1.412
1EthB H227 1.056 2.343 1.587
2Eth C18 1.002 2.154 1.500
2EthH119 0.948 2.117 1.587
2EthH12 10 0.948 2.117 1.412
2Eth C2 11 1.144 2.098 1.500
2EthH21 12 1.198 2.135 1.412
2EthH22 13 1.198 2.135 1.587
3Eth C1 14 1.145 1.946 1.500
3EthH11 15 1.091 1.909 1
[gmx-users] building up a long polymer chain
Hello Justin, As you pointed out at the end of former message my real problem is generation of a properly formatted structure file for PE. Within last few weeks I tried to obtain the structure file using that known link... but that was not helpful to me since those residues need atom numbering..Hdb file was not helpful either because I think I need to have a structure file with only coordinates of carbon atoms (hdb adds H ). ...That coordinate file I dont know how to get. I tried x2top command to generate top file and I got LINCS error. I followd the tips you had given before on how to diagnose a crashing system and thats why I suspect top file is not produced properly when I have no atom numbering in coordinate file. Now I am following your suggestion to use genconf command to build up my polymer. The distance between C -C atoms in ethylene is 1.52 A. So I considred 0.76 A as distance from each side, and 1.52+ 2*0.76=3.04 A as box size. In the command line below I entered 0.304 to convert to nm. Please see below: Initsial pdb file: HETATM1 C1 EthB1 2.739 2.554 -0.012 0.00 -0.39 C HETATM2 H11 EthB1 2.736 3.644 -0.012 0.00 0.13 H HETATM3 H12 EthB1 2.190 2.217 -0.893 0.00 0.13 H HETATM4 H13 EthB1 2.190 2.217 0.868 0.00 0.13 H HETATM5 C2 EthB1 4.155 1.993 -0.012 0.00 -0.26 C HETATM6 H21 EthB1 4.696 2.362 -0.887 0.00 0.13 H HETATM7 H22 EthB1 4.696 2.362 0.862 0.00 0.13 H END editconf -f PEmonomer.pdb -o PEmonomer.gro -box 0.304 0.304 0.304 -angles 90 90 90 -d 0.076 7 1EthBC11 0.141 0.166 0.164 1EthB H112 0.141 0.275 0.164 1EthB H123 0.086 0.132 0.076 1EthB H134 0.086 0.132 0.252 1EthBC25 0.282 0.110 0.164 1EthB H216 0.337 0.147 0.077 1EthB H227 0.337 0.147 0.251 0.40260 0.31710 0.32810 0.0 0.0 0.0 0.0 0.0 0.0 genconf -f PEmonomer.gro -sort -o PEsort -nbox 5 I use -sort to align the molecule with X coordinate and want to replicate 5 boxes. Am I using correctly the -sort option? What I get is: 8875 1EthBC11 0.086 0.132 0.252 0. 0. 0. 1EthB H112 0.282 0.110 0.164 0. 0. 0. 1EthB H123 0.337 0.147 0.077 0. 0. 0. 1EthB H134 0.086 0.132 0.404 0. 0. 0. 1EthBC25 0.086 0.132 0.580 0. 0. 0. 1EthB H216 0.282 0.110 0.492 0. 0. 0. 1EthB H227 0.086 0.132 1.236 0. 0. 0. 2EthBC18 0.282 0.110 1.148 0. 0. 0. 2EthB H119 0.337 0.147 1.061 0. 0. 0. 2EthB H12 10 0.086 0.132 1.388 0. 0. 0. 2EthB H13 11 0.086 0.132 1.564 0. 0. 0. 2EthBC2 12 0.282 0.110 1.476 0. 0. 0. 2EthB H21 13 0.086 0.449 0.580 0. 0. 0. 2EthB H22 14 0.282 0.427 0.492 0. 0. 0. 3EthBC1 15 0.337 0.464 0.405 0. 0. 0. 3EthB H11 16 0.086 0.449 0.732 0. 0. 0. To me what I have done is not right. 1- I am replicating CH3CH, while what I need is CH2CH2. Even when I do this I need to somehow add in CH3 to both ends! Please guide me on this issue 2- I am sure something is wrong. When I use -box 5 I get 8875 monomer units! Thank you, Moeed -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] building up a long polymer chain
Hello Justin, I created structure file for a 4-carbon repeating unit as follows: HETATM1 CAA DRG 1 14.260 -4.270 0.000 1.00 20.00 C HETATM2 1HAA DRG 1 14.175 -3.426 0.530 1.00 20.00 H HETATM3 2HAA DRG 1 15.050 -4.790 0.326 1.00 20.00 H HETATM4 3HAA DRG 1 14.385 -4.045 -0.966 1.00 20.00 H HETATM5 CAB DRG 1 12.990 -5.110 0.170 1.00 20.00 C HETATM6 1HAB DRG 1 12.205 -4.581 -0.153 1.00 20.00 H HETATM7 2HAB DRG 1 12.871 -5.326 1.139 1.00 20.00 H HETATM8 CAC DRG 1 13.070 -6.410 -0.620 1.00 20.00 C HETATM9 1HAC DRG 1 13.855 -6.939 -0.297 1.00 20.00 H HETATM 10 2HAC DRG 1 13.189 -6.194 -1.589 1.00 20.00 H HETATM 11 CAD DRG 1 11.800 -7.250 -0.450 1.00 20.00 C HETATM 12 1HAD DRG 1 11.885 -8.094 -0.980 1.00 20.00 H HETATM 13 2HAD DRG 1 11.675 -7.475 0.516 1.00 20.00 H HETATM 14 3HAD DRG 1 11.010 -6.730 -0.776 1.00 20.00 H I renamed the atoms and removed one hydrogen atoms from both ends to get repeating unit. CH2CH2, 1- I am not able to produce the repeating unit C2H4 in PRODRG. It adds the third H automatically. I dont know anyother way but removing the third H from structure file by hand.. Then I mesaured the C1 To C4 distance which is 0.388 A. editconf -f prodrg.pdb -o prodrg.gro -box 0.388 -bt cubic 12 1DRG C11 0.208 0.006 0.242 1DRGH112 0.158 0.010 0.328 1DRGH123 0.149 -0.030 0.170 1DRG C24 0.255 0.148 0.203 1DRGH215 0.305 0.143 0.116 1DRGH226 0.314 0.184 0.274 1DRG C37 0.133 0.240 0.186 1DRGH318 0.083 0.245 0.272 1DRGH329 0.074 0.204 0.114 1DRG C4 10 0.179 0.382 0.147 1DRGH41 11 0.239 0.418 0.218 1DRGH42 12 0.230 0.378 0.060 0.38800 0.38800 0.38800 then : genconf -f prodrg.gro -o rep.gro -nbox 1 5 1 2- The problem here is that one CH2 unit with 2 H atoms is falling on the next repeating unit in the next box. i.e 4 H atoms and C atoms are overlapping... as shown below: H H H *H H* H H H | | | | | | | | C-C-C-*CC*-C-C-C | | | | | | | | H H H *H H* H H H Do you think I should use -d option? Please guide me.. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] building up a long polymer chain
Moeed wrote: for PE. or maybe this dies not affect the results since charges and mass are the same..?! You can set the charges to whatever you want them to be, so this is no issue at all. Also: can opls_157 be used for both CH3 & CH2,on PE chain? what is the suitable atom type for carbon atoms on PE chain? The nonbonded parameters (sigma and epsilon) for opls_135 and opls_157 are identical. I don't know why there are different types, but they are the same. Check ffoplsaanb.itp and you will see. The top file I got has contains exactly the same listing of [bonds] [pairs] [angles] [dihedrals] as the one I got from the structure file for which I did the numbering by hand. But I am unsure of the forcefield parameters if they are extracted from itp file properly because after doing energy minimization step I get LINCS error. I don't fully understand what you did or what you think is wrong, but I do recall giving you some very thorough procedures to go through to diagnose a crashing system. I even updated the wiki to keep track of all the tips I gave you. Q 2-1 Please kindly furnish me with your comments on this issue. *I need a residue for internal ethylene monomer in rtp file which depends as less as possible on atoms numbering (H11,...). *I think the solution will help many gmx users dealing with polymers. what would be the best approach? To build a long polymer chain, it should be possible by generating a coordinate file of one monomer that is aligned with one of the principal axes and positioned such that its atoms are half a bond length from the edges of the box. Then use genconf -nbox to replicate this system in one direction and you'll have as long a chain as you want, correctly numbered and named, and if you've done your geometry right, the structure will even be in a reasonable configuration. If you want to use .rtp files to create a topology, atom naming is required to be consistent with the structure file. There is no way around this. The hydrogen atoms are actually very easy to deal with if you have an appropriate .hdb file, which is provided in the example you've been using for several weeks now. So you really don't even need H atoms in your input file, just appropriately-named carbons. my current internal repeating unit has numbering of atoms: [Eth ] [ atoms ] C1opls_136-0.1201 H11 opls_140 0.0601 H12 opls_140 0.0601 C2opls_136-0.1202 H21 opls_140 0.0602 H22 opls_140 0.0602 [ bonds ] C1-C2 C1H11 C1H12 C1C2 C2H21 C2H22 C2+C1 Q 2-2. Does x2top command have advantage over pdb2gmx command with regards to atom numbering? It seems like your first real problem is creating a properly-formatted coordinate file. If you have to add in residue names yourself and rename all of the atoms yourself, then that's more trouble than its worth. See the above comment about genconf. -Justin Many many thanks, Best, Moeed -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] building up a long polymer chain
Moeed wrote: Hello Justin, As you pointed out at the end of former message my real problem is generation of a properly formatted structure file for PE. Within last few weeks I tried to obtain the structure file using that known link... but that was not helpful to me since those residues need atom numbering..Hdb file was not helpful either because I think I need to have a structure file with only coordinates of carbon atoms (hdb adds H ). ...That coordinate file I dont know how to get. http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources With both PRODRG and xLeap you should be able to easily build a short repeat unit. You will have to rename the constituent atoms, but at least the coordinate files are syntactically correct. I tried x2top command to generate top file and I got LINCS error. I followd the tips you had given before on how to diagnose a crashing system and thats why I suspect top file is not produced properly when I have no atom numbering in coordinate file. Now I am following your Well, I have never dealt with something like that, but if you're coordinate file is useless, then so too will the topology, likely. suggestion to use genconf command to build up my polymer. The distance between C -C atoms in ethylene is 1.52 A. So I considred 0.76 A as distance from each side, and 1.52+ 2*0.76=3.04 A as box size. In the command line below I entered 0.304 to convert to nm. Please see below: Initsial pdb file: HETATM1 C1 EthB1 2.739 2.554 -0.012 0.00 -0.39 C HETATM2 H11 EthB1 2.736 3.644 -0.012 0.00 0.13 H HETATM3 H12 EthB1 2.190 2.217 -0.893 0.00 0.13 H HETATM4 H13 EthB1 2.190 2.217 0.868 0.00 0.13 H HETATM5 C2 EthB1 4.155 1.993 -0.012 0.00 -0.26 C HETATM6 H21 EthB1 4.696 2.362 -0.887 0.00 0.13 H HETATM7 H22 EthB1 4.696 2.362 0.862 0.00 0.13 H END editconf -f PEmonomer.pdb -o PEmonomer.gro -box 0.304 0.304 0.304 -angles 90 90 90 -d 0.076 Going by the nomenclature of the system we've been discussing for the last eternity, EthB is a "beginning" residue, i.e. CH3-CH2-, when what you want to be using is Eth, which is a -CH2-CH2- unit. Once you've built the coordinate file, change the names of the beginning and end residues and process the structure with pdb2gmx to build back the right hydrogens. By specifying both -box and -d, you are adding extra space in the box. The use of -angles is not necessary, and somehow you are not getting a cubic box: 0.40260 0.31710 0.32810 0.0 0.0 0.0 0.0 0.0 0.0 The proper command for what you want is: editconf -f PEmonomer.pdb -o PEmonomer.gro -box 0.304 -bt cubic genconf -f PEmonomer.gro -sort -o PEsort -nbox 5 I use -sort to align the molecule with X coordinate and want to replicate 5 boxes. Am I using correctly the -sort option? What I get is: 8875 1EthBC11 0.086 0.132 0.252 0. 0. 0. 1EthB H112 0.282 0.110 0.164 0. 0. 0. 1EthB H123 0.337 0.147 0.077 0. 0. 0. 1EthB H134 0.086 0.132 0.404 0. 0. 0. 1EthBC25 0.086 0.132 0.580 0. 0. 0. 1EthB H216 0.282 0.110 0.492 0. 0. 0. 1EthB H227 0.086 0.132 1.236 0. 0. 0. 2EthBC18 0.282 0.110 1.148 0. 0. 0. 2EthB H119 0.337 0.147 1.061 0. 0. 0. 2EthB H12 10 0.086 0.132 1.388 0. 0. 0. 2EthB H13 11 0.086 0.132 1.564 0. 0. 0. 2EthBC2 12 0.282 0.110 1.476 0. 0. 0. 2EthB H21 13 0.086 0.449 0.580 0. 0. 0. 2EthB H22 14 0.282 0.427 0.492 0. 0. 0. 3EthBC1 15 0.337 0.464 0.405 0. 0. 0. 3EthB H11 16 0.086 0.449 0.732 0. 0. 0. To me what I have done is not right. 1- I am replicating CH3CH, while what I need is CH2CH2. Even when I do this I need to somehow add in CH3 to both ends! Please guide me on this issue See above. 2- I am sure something is wrong. When I use -box 5 I get 8875 monomer units! Yes, because when a GROMACS command expects a vector quantity, and receives only a scalar, it is applied uniformly in all directions. This is documented in the manual. I also see no purpose whatsoever to using -sort. What you need is: genconf -f PEmonomer.gro -o PEchain.gro -nbox 5 1 1 -Justin Thank you, Moeed -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 23
Re: [gmx-users] building up a long polymer chain
Moeed wrote: Hello Justin, I created structure file for a 4-carbon repeating unit as follows: HETATM1 CAA DRG 1 14.260 -4.270 0.000 1.00 20.00 C HETATM2 1HAA DRG 1 14.175 -3.426 0.530 1.00 20.00 H HETATM3 2HAA DRG 1 15.050 -4.790 0.326 1.00 20.00 H HETATM4 3HAA DRG 1 14.385 -4.045 -0.966 1.00 20.00 H HETATM5 CAB DRG 1 12.990 -5.110 0.170 1.00 20.00 C HETATM6 1HAB DRG 1 12.205 -4.581 -0.153 1.00 20.00 H HETATM7 2HAB DRG 1 12.871 -5.326 1.139 1.00 20.00 H HETATM8 CAC DRG 1 13.070 -6.410 -0.620 1.00 20.00 C HETATM9 1HAC DRG 1 13.855 -6.939 -0.297 1.00 20.00 H HETATM 10 2HAC DRG 1 13.189 -6.194 -1.589 1.00 20.00 H HETATM 11 CAD DRG 1 11.800 -7.250 -0.450 1.00 20.00 C HETATM 12 1HAD DRG 1 11.885 -8.094 -0.980 1.00 20.00 H HETATM 13 2HAD DRG 1 11.675 -7.475 0.516 1.00 20.00 H HETATM 14 3HAD DRG 1 11.010 -6.730 -0.776 1.00 20.00 H I renamed the atoms and removed one hydrogen atoms from both ends to get repeating unit. CH2CH2, 1- I am not able to produce the repeating unit C2H4 in PRODRG. It adds the third H automatically. I dont know anyother way but removing the third H from structure file by hand.. Then I mesaured the C1 To C4 distance which is 0.388 A. editconf -f prodrg.pdb -o prodrg.gro -box 0.388 -bt cubic 12 1DRG C11 0.208 0.006 0.242 1DRGH112 0.158 0.010 0.328 1DRGH123 0.149 -0.030 0.170 1DRG C24 0.255 0.148 0.203 1DRGH215 0.305 0.143 0.116 1DRGH226 0.314 0.184 0.274 1DRG C37 0.133 0.240 0.186 1DRGH318 0.083 0.245 0.272 1DRGH329 0.074 0.204 0.114 1DRG C4 10 0.179 0.382 0.147 1DRGH41 11 0.239 0.418 0.218 1DRGH42 12 0.230 0.378 0.060 0.38800 0.38800 0.38800 then : genconf -f prodrg.gro -o rep.gro -nbox 1 5 1 2- The problem here is that one CH2 unit with 2 H atoms is falling on the next repeating unit in the next box. i.e 4 H atoms and C atoms are overlapping... as shown below: H H H *H H* H H H | | | | | | | | C-C-C-*CC*-C-C-C | | | | | | | | H H H *H H* H H H Do you think I should use -d option? As I've said twice now, use either -box or -d to set an appropriately-sized unit cell. If you've measured a C...C distance of 0.388 nm, you've left no space for the bond that will occur to the next unit, so naturally you're seeing overlap. You've simply made your box too small. -Justin Please guide me.. Thanks -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
