Re: Fwd: Fwd: [gmx-users] scripts to generate topology CG
Francesco Pietra wrote: I was asked to submit details of the procedure to get a solvated CG system in order to see if help to correct the procedure is feasible. Is the described procedure still insufficient? thanks for answering I posted several suggestions and some questions when you last posted this information: http://lists.gromacs.org/pipermail/gmx-users/2009-October/046189.html Did any of that work? Did you try what I suggested with editconf? I think the problem with using genbox as you have described is that the system is tiled within a newly-defined box, placing your system in the corner as you described. Using editconf should eliminate this problem. -Justin francesco -- Forwarded message -- From: Francesco Pietra Date: Sun, Oct 25, 2009 at 6:22 PM Subject: Re: Fwd: [gmx-users] scripts to generate topology CG To: jalem...@vt.edu, Discussion list for GROMACS users On Fri, Oct 23, 2009 at 5:32 PM, Justin A. Lemkul wrote: Francesco Pietra wrote: grep W solvated.gro | wc -l and use that number in the topology? I forgot to add that the graphic program uses the above grep command, I don't understand this statement. giving the same number of W as the line command. The number of DCCP is diminished by those deleted in inserting the protein, but the grompp command complains that .gro does not matches .top. If no further water is added graphically, everything works. This is where exact commands (in sequence) really help, or at least a stepwise procedure. Are you adding a protein into a box that contains DCCP+water, or are you inserting the protein into DCCP, then adding water? What is the exact error that grompp is giving you? That the number of coordinates don't match? atom names don't match? What I did follows. I am using the actual filenames and page numbers for my reference. (1) getting mod21.cg.pdb from mod21.pdb by using the martini awk script (p. 4). (2) getting mod21.itp by using dssp, fasta, seq2itp.pl (p. 4). (3) downloading dppc_bilayer.gro, editconf to get dppc_bilayer.pdb (p. 4). (4) inserting the pore region of the cg protein into the bilayer in the obvious orientation, then removing all dppc superimposed to the protein plus an extra margin of 10A, to get mod21.aligned.pdb and dppc.aligned.pdb (according to as described for all-atoms in the paper I referred to in this thread) (p. 4) (5) genbox -cp mod21.aligned.pdb -cs dppc.aligned.pdb -box 11 11 11 -o mod21+dccp.box.pdb resulted in the protein at a corner of the cubic box. This is probably because I was using a homology model, i.e., there was no CRYSTAL record. It was nonetheless surprising because the two .pdb files to combine had the same box size (p. 5). (6) Cut-and-paste adding mod21.aligned.pdb to dppc.aligned.pdb resulted in a correct insertion of the pore region into the bilayer, the latter correctly oriented. Filename dppc+mod21.pdb (p. 6). The bilayer originally was made of 128 dppc and 2000 W. After insertion of the protein, the system was 1 multimeric protein, 85 dppc and 1767 W (taking into account that there are 12 atoms per dppc). (7) genbox -cp dppc+mod21.pdb -cs water-1bar.303K.gro -box 11 20 11 -o dppc+mod21+W.box.pdb resulted in the protein at a corner of the solvating box, which only comprised the pore region inserted into the bilayer. I.e., the large non-pore region of the protein was not solvated. On making the box bigger and bigger also the non-pore region was solvated but the pore region exited the bilayer and entered the water region. Which situation could not be accepted (pp. 8-9). I was unable to detect whether I was using wrong commands with genbox, and therefore I abandoned genbox. (8) Starting from dppc+mod21.pdb (from step 6) I tried solvating the non-pore region of the protein-dppc ensemble by adding a preformed box of water (that is, using the methodology of step 4). Thus, dppc+mod21.pd was aligned with a water box of 5400 W, removing all W superimposed to the non-pore region of mod21+dppc, plus a margin of 10A. The ensemble (filename dppc+mod21+W.gro) opens correctly in VMD (or as corresponding .pdb file in CHIMERA), that is, the non-pore region is solvated (pp. 11-12). In my hands, the .pdb file describing this ensemble did not allow to generate a .tpr file. The ensemble was made of Protein 1 (multimeric) DPPC 85 W 6008 which data were used for the .top file. Command $ grompp -f minimize.mdp -c dppc+mod21+W.gro -p dppc+mod21+W.top -o minimize.tpr resulted in error: number of coordinates in coordinate file (dppc+mod21+W.gro 5662) does not match topology (dppc+mod21+W.top, 9903) (p. 19). (9) Starting directly from dppc+mod21.pdb (from step 6), commad $ genbox -cp dppc+mod21.pdb -box 10 17 10 -o dppc+mod21.gro 5662 atoms in 3122 residues Volume: 1700 nm^3 Density: 99.5996 SOL: 0 followed by command $ grompp -f minimize.mdp -c dppc+mod21.gr
Fwd: Fwd: [gmx-users] scripts to generate topology CG
I was asked to submit details of the procedure to get a solvated CG system in order to see if help to correct the procedure is feasible. Is the described procedure still insufficient? thanks for answering francesco -- Forwarded message -- From: Francesco Pietra Date: Sun, Oct 25, 2009 at 6:22 PM Subject: Re: Fwd: [gmx-users] scripts to generate topology CG To: jalem...@vt.edu, Discussion list for GROMACS users On Fri, Oct 23, 2009 at 5:32 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: > >>> grep W solvated.gro | wc -l >>> >>> and use that number in the topology? >> >> I forgot to add that the graphic program uses the above grep command, > > I don't understand this statement. > >> giving the same number of W as the line command. The number of DCCP is >> diminished by those deleted in inserting the protein, but the grompp >> command complains that .gro does not matches .top. If no further water >> is added graphically, everything works. > > This is where exact commands (in sequence) really help, or at least a > stepwise procedure. Are you adding a protein into a box that contains > DCCP+water, or are you inserting the protein into DCCP, then adding water? > > What is the exact error that grompp is giving you? That the number of > coordinates don't match? atom names don't match? What I did follows. I am using the actual filenames and page numbers for my reference. (1) getting mod21.cg.pdb from mod21.pdb by using the martini awk script (p. 4). (2) getting mod21.itp by using dssp, fasta, seq2itp.pl (p. 4). (3) downloading dppc_bilayer.gro, editconf to get dppc_bilayer.pdb (p. 4). (4) inserting the pore region of the cg protein into the bilayer in the obvious orientation, then removing all dppc superimposed to the protein plus an extra margin of 10A, to get mod21.aligned.pdb and dppc.aligned.pdb (according to as described for all-atoms in the paper I referred to in this thread) (p. 4) (5) genbox -cp mod21.aligned.pdb -cs dppc.aligned.pdb -box 11 11 11 -o mod21+dccp.box.pdb resulted in the protein at a corner of the cubic box. This is probably because I was using a homology model, i.e., there was no CRYSTAL record. It was nonetheless surprising because the two .pdb files to combine had the same box size (p. 5). (6) Cut-and-paste adding mod21.aligned.pdb to dppc.aligned.pdb resulted in a correct insertion of the pore region into the bilayer, the latter correctly oriented. Filename dppc+mod21.pdb (p. 6). The bilayer originally was made of 128 dppc and 2000 W. After insertion of the protein, the system was 1 multimeric protein, 85 dppc and 1767 W (taking into account that there are 12 atoms per dppc). (7) genbox -cp dppc+mod21.pdb -cs water-1bar.303K.gro -box 11 20 11 -o dppc+mod21+W.box.pdb resulted in the protein at a corner of the solvating box, which only comprised the pore region inserted into the bilayer. I.e., the large non-pore region of the protein was not solvated. On making the box bigger and bigger also the non-pore region was solvated but the pore region exited the bilayer and entered the water region. Which situation could not be accepted (pp. 8-9). I was unable to detect whether I was using wrong commands with genbox, and therefore I abandoned genbox. (8) Starting from dppc+mod21.pdb (from step 6) I tried solvating the non-pore region of the protein-dppc ensemble by adding a preformed box of water (that is, using the methodology of step 4). Thus, dppc+mod21.pd was aligned with a water box of 5400 W, removing all W superimposed to the non-pore region of mod21+dppc, plus a margin of 10A. The ensemble (filename dppc+mod21+W.gro) opens correctly in VMD (or as corresponding .pdb file in CHIMERA), that is, the non-pore region is solvated (pp. 11-12). In my hands, the .pdb file describing this ensemble did not allow to generate a .tpr file. The ensemble was made of Protein 1 (multimeric) DPPC 85 W 6008 which data were used for the .top file. Command $ grompp -f minimize.mdp -c dppc+mod21+W.gro -p dppc+mod21+W.top -o minimize.tpr resulted in error: number of coordinates in coordinate file (dppc+mod21+W.gro 5662) does not match topology (dppc+mod21+W.top, 9903) (p. 19). (9) Starting directly from dppc+mod21.pdb (from step 6), commad $ genbox -cp dppc+mod21.pdb -box 10 17 10 -o dppc+mod21.gro 5662 atoms in 3122 residues Volume: 1700 nm^3 Density: 99.5996 SOL: 0 followed by command $ grompp -f minimize.mdp -c dppc+mod21.gro -p dppc+mod21.top -o minimize.tpr where, for the .top file, [molecule] Protein 1 DPPC 85 W 1767 (derived as indicated at step 6) generated correctly the .tpr file (p. 20). ... I hope to have illustrated in sufficient details the procedure so as my mistakes could be detected. thanks for help francesco
Re: Fwd: [gmx-users] scripts to generate topology CG
Francesco Pietra wrote: On Fri, Oct 23, 2009 at 5:32 PM, Justin A. Lemkul wrote: Francesco Pietra wrote: grep W solvated.gro | wc -l and use that number in the topology? I forgot to add that the graphic program uses the above grep command, I don't understand this statement. giving the same number of W as the line command. The number of DCCP is diminished by those deleted in inserting the protein, but the grompp command complains that .gro does not matches .top. If no further water is added graphically, everything works. This is where exact commands (in sequence) really help, or at least a stepwise procedure. Are you adding a protein into a box that contains DCCP+water, or are you inserting the protein into DCCP, then adding water? What is the exact error that grompp is giving you? That the number of coordinates don't match? atom names don't match? What I did follows. I am using the actual filenames and page numbers for my reference. (1) getting mod21.cg.pdb from mod21.pdb by using the martini awk script (p. 4). (2) getting mod21.itp by using dssp, fasta, seq2itp.pl (p. 4). (3) downloading dppc_bilayer.gro, editconf to get dppc_bilayer.pdb (p. 4). (4) inserting the pore region of the cg protein into the bilayer in the obvious orientation, then removing all dppc superimposed to the protein plus an extra margin of 10A, to get mod21.aligned.pdb and dppc.aligned.pdb (according to as described for all-atoms in the paper I referred to in this thread) (p. 4) (5) genbox -cp mod21.aligned.pdb -cs dppc.aligned.pdb -box 11 11 11 -o mod21+dccp.box.pdb resulted in the protein at a corner of the cubic box. This is probably because I was using a homology model, i.e., there was no CRYSTAL record. It was nonetheless surprising because the two .pdb files to combine had the same box size (p. 5). Box manipulation can be tricky. I would recommend doing the alignment with editconf, for example, to place the bilayer and protein centers at the center of the box, you would issue: editconf -f mod21.aligned.pdb -o mod21.aligned.center.pdb -c -box 11 -bt cubic And analogously for the bilayer. If the center must be shifted relative to the box center, you can supply to exact coordinates with editconf -center. (6) Cut-and-paste adding mod21.aligned.pdb to dppc.aligned.pdb resulted in a correct insertion of the pore region into the bilayer, the latter correctly oriented. Filename dppc+mod21.pdb (p. 6). The bilayer originally was made of 128 dppc and 2000 W. After insertion of the protein, the system was 1 multimeric protein, 85 dppc and 1767 W (taking into account that there are 12 atoms per dppc). (7) genbox -cp dppc+mod21.pdb -cs water-1bar.303K.gro -box 11 20 11 -o dppc+mod21+W.box.pdb resulted in the protein at a corner of the solvating box, which only comprised the pore region inserted into the bilayer. I.e., the large non-pore region of the protein was not solvated. On making the box bigger and bigger also the non-pore region was solvated but the pore region exited the bilayer and entered the water region. Which situation could not be accepted (pp. 8-9). I think genbox is inducing this effect because it is trying to assemble your system within the -box you have defined. I am not aware of any known issues with using genbox -box, but as a matter of routine, I always define the box with editconf prior to running genbox. Again, I don't know of anything that is broken about genbox, but it would be worthwhile to eliminate this as a potential problem. I was unable to detect whether I was using wrong commands with genbox, and therefore I abandoned genbox. (8) Starting from dppc+mod21.pdb (from step 6) I tried solvating the non-pore region of the protein-dppc ensemble by adding a preformed box of water (that is, using the methodology of step 4). Thus, dppc+mod21.pd was aligned with a water box of 5400 W, removing all W superimposed to the non-pore region of mod21+dppc, plus a margin of 10A. The ensemble (filename dppc+mod21+W.gro) opens correctly in VMD (or as corresponding .pdb file in CHIMERA), that is, the non-pore region is solvated (pp. 11-12). In my hands, the .pdb file describing this ensemble did not allow to generate a .tpr file. The ensemble was made of Protein 1 (multimeric) DPPC 85 W 6008 which data were used for the .top file. Command $ grompp -f minimize.mdp -c dppc+mod21+W.gro -p dppc+mod21+W.top -o minimize.tpr resulted in error: number of coordinates in coordinate file (dppc+mod21+W.gro 5662) does not match topology (dppc+mod21+W.top, 9903) (p. 19). Can you post the first and last few lines of dppc+mod21+W.gro (i.e., "head dppc+mod21+W.gro" and "tail dppc+mod21+W.gro")? -Justin (9) Starting directly from dppc+mod21.pdb (from step 6), commad $ genbox -cp dppc+mod21.pdb -box 10 17 10 -o dppc+mod21.gro 5662 atoms in 3122 residues Volume: 1700 nm^3 Density: 99.5996 SOL: 0 fo
Re: Fwd: [gmx-users] scripts to generate topology CG
On Fri, Oct 23, 2009 at 5:32 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: > >>> grep W solvated.gro | wc -l >>> >>> and use that number in the topology? >> >> I forgot to add that the graphic program uses the above grep command, > > I don't understand this statement. > >> giving the same number of W as the line command. The number of DCCP is >> diminished by those deleted in inserting the protein, but the grompp >> command complains that .gro does not matches .top. If no further water >> is added graphically, everything works. > > This is where exact commands (in sequence) really help, or at least a > stepwise procedure. Are you adding a protein into a box that contains > DCCP+water, or are you inserting the protein into DCCP, then adding water? > > What is the exact error that grompp is giving you? That the number of > coordinates don't match? atom names don't match? What I did follows. I am using the actual filenames and page numbers for my reference. (1) getting mod21.cg.pdb from mod21.pdb by using the martini awk script (p. 4). (2) getting mod21.itp by using dssp, fasta, seq2itp.pl (p. 4). (3) downloading dppc_bilayer.gro, editconf to get dppc_bilayer.pdb (p. 4). (4) inserting the pore region of the cg protein into the bilayer in the obvious orientation, then removing all dppc superimposed to the protein plus an extra margin of 10A, to get mod21.aligned.pdb and dppc.aligned.pdb (according to as described for all-atoms in the paper I referred to in this thread) (p. 4) (5) genbox -cp mod21.aligned.pdb -cs dppc.aligned.pdb -box 11 11 11 -o mod21+dccp.box.pdb resulted in the protein at a corner of the cubic box. This is probably because I was using a homology model, i.e., there was no CRYSTAL record. It was nonetheless surprising because the two .pdb files to combine had the same box size (p. 5). (6) Cut-and-paste adding mod21.aligned.pdb to dppc.aligned.pdb resulted in a correct insertion of the pore region into the bilayer, the latter correctly oriented. Filename dppc+mod21.pdb (p. 6). The bilayer originally was made of 128 dppc and 2000 W. After insertion of the protein, the system was 1 multimeric protein, 85 dppc and 1767 W (taking into account that there are 12 atoms per dppc). (7) genbox -cp dppc+mod21.pdb -cs water-1bar.303K.gro -box 11 20 11 -o dppc+mod21+W.box.pdb resulted in the protein at a corner of the solvating box, which only comprised the pore region inserted into the bilayer. I.e., the large non-pore region of the protein was not solvated. On making the box bigger and bigger also the non-pore region was solvated but the pore region exited the bilayer and entered the water region. Which situation could not be accepted (pp. 8-9). I was unable to detect whether I was using wrong commands with genbox, and therefore I abandoned genbox. (8) Starting from dppc+mod21.pdb (from step 6) I tried solvating the non-pore region of the protein-dppc ensemble by adding a preformed box of water (that is, using the methodology of step 4). Thus, dppc+mod21.pd was aligned with a water box of 5400 W, removing all W superimposed to the non-pore region of mod21+dppc, plus a margin of 10A. The ensemble (filename dppc+mod21+W.gro) opens correctly in VMD (or as corresponding .pdb file in CHIMERA), that is, the non-pore region is solvated (pp. 11-12). In my hands, the .pdb file describing this ensemble did not allow to generate a .tpr file. The ensemble was made of Protein 1 (multimeric) DPPC 85 W 6008 which data were used for the .top file. Command $ grompp -f minimize.mdp -c dppc+mod21+W.gro -p dppc+mod21+W.top -o minimize.tpr resulted in error: number of coordinates in coordinate file (dppc+mod21+W.gro 5662) does not match topology (dppc+mod21+W.top, 9903) (p. 19). (9) Starting directly from dppc+mod21.pdb (from step 6), commad $ genbox -cp dppc+mod21.pdb -box 10 17 10 -o dppc+mod21.gro 5662 atoms in 3122 residues Volume: 1700 nm^3 Density: 99.5996 SOL: 0 followed by command $ grompp -f minimize.mdp -c dppc+mod21.gro -p dppc+mod21.top -o minimize.tpr where, for the .top file, [molecule] Protein 1 DPPC 85 W 1767 (derived as indicated at step 6) generated correctly the .tpr file (p. 20). ... I hope to have illustrated in sufficient details the procedure so as my mistakes could be detected. thanks for help francesco > > -Justin > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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 list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before pos
Re: Fwd: [gmx-users] scripts to generate topology CG
Francesco Pietra wrote: grep W solvated.gro | wc -l and use that number in the topology? I forgot to add that the graphic program uses the above grep command, I don't understand this statement. giving the same number of W as the line command. The number of DCCP is diminished by those deleted in inserting the protein, but the grompp command complains that .gro does not matches .top. If no further water is added graphically, everything works. This is where exact commands (in sequence) really help, or at least a stepwise procedure. Are you adding a protein into a box that contains DCCP+water, or are you inserting the protein into DCCP, then adding water? What is the exact error that grompp is giving you? That the number of coordinates don't match? atom names don't match? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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
Fwd: [gmx-users] scripts to generate topology CG
-- Forwarded message -- From: Francesco Pietra Date: Fri, Oct 23, 2009 at 5:01 PM Subject: Re: [gmx-users] scripts to generate topology CG To: jalem...@vt.edu, Discussion list for GROMACS users On Fri, Oct 23, 2009 at 4:14 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: >> >> Hello Sunny: >> I had already generated a valid .itp file for my protein using >> seq2itp. That .itp works for both the protein itself and the protein >> graphically inserted into a bilayer. When I add graphically further >> water it does not work any more. I thought there is something else >> that manages water without putting it everywhere. That script does not >> help. >> > > In order to get a solution to your problem, I think you're going to have to > explain your methodology more clearly, including command lines and actual > error messages. How are you adding water "graphically"? Is genbox not > working? Can you not simply grep for the number of water molecules, i.e.: > > grep W solvated.gro | wc -l > > and use that number in the topology? I forgot to add that the graphic program uses the above grep command, giving the same number of W as the line command. The number of DCCP is diminished by those deleted in inserting the protein, but the grompp command complains that .gro does not matches .top. If no further water is added graphically, everything works. > > -Justin I'll organize to explain in more details. The methodology (all-atoms) is explained in a few papers of mine and supplementary material, for example: F. Pietra “ Docking and MD simulations of the interaction of the tarantula peptide psalmotoxin‑1 with ASIC1a channels using a homology model” J. Chem. Inf. Model. 2009, 49, 972-977. thanks francesco > >> thanks >> francesco >> >> On Wed, Oct 21, 2009 at 3:46 PM, sunny mishra >> wrote: >>> >>> There is a seq2itp.pl script provided by martini folks in their >>> website. You can get it from there. >>> >>> Sunny >>> >>> On Wed, Oct 21, 2009 at 9:42 AM, Francesco Pietra >>> wrote: Hi: I am looking for scripts that generate topology in coarse grained. Thanks for indications. francesco pietra ___ gmx-users mailing list gmx-us...@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 mailing list gmx-us...@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 mailing list gmx-us...@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 >> > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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 list gmx-us...@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 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