Re: Fw: [gmx-users] position restraints
On Tue, Mar 26, 2013 at 1:01 PM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: Have a look at processed topology file here please; I see that position restraints are brought after chain_A but not brought after chain_B. With these settings: ; Include chain topologies #ifdef POSRES #include topol_Protein_chain_A.itp #include protein_chain_A_posre.itp #endif #ifdef POSRES #include topol_Protein_chain_B.itp #include protein_chain_B_posre.itp #endif The above approach is incorrect. The inclusion of protein topologies is dependent upon using position restraints? That's certainly not right, especially if you ever want to run a simulation without restraints. The following is the correct approach: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRES #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRES #include protein_chain_B_posre.itp #endif Also adding define = -DPOSRES_LIPID -DPOSRES , I get this processed.top: #grompp -f nvt.mdp -c minim.gro -p topol.top -n index.ndx -o nvt.tpr -pp THIS IS THE PROCESSED TOPOLOGY: ;File 'topol.top' was generated ;By user: shima (1000) ;On host: linux-cbyo.site ;At date: Wed Dec 12 12:17:51 2012 ; ;This is a standalone topology file ; ;It was generated using program: ;pdb2gmx - VERSION 4.5.5 ; ;Command line was: ;pdb2gmx -f dimer-rotated.pdb -o dimer-processed.pdb -ter -water tip3p ; ;Force field was read from current directory or a relative path - path added. ; ; Include forcefield parameters ; Conversion of CHARMM36 parameters to GROMACS format by Thomas Piggot, July 2010. ; Also added some parameters from later CHARMM27 versions, such as those for the PS headgroup. ; ; If you use these parameters please check out the forcefield.doc for papers to cite [ defaults ] ; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ 12yes1.01.0 ; ; Added new and changed old atomtypes and pairtypes (OSL, OSLP, HBL and CCL) - Thomas Pigot July 2010 ; [ atomtypes ] ;nameat.nummasschargeptypesigmaepsilon C612.011000.51A0.3563594872560.46024 CA612.01100-0.115A0.3550053212050.29288 CC612.011000.62A0.3563594872560.29288 CD612.011000.000A0.3563594872560.29288 ; partial charge def not found CE1612.011000.000A0.3723956641830.284512 ; partial charge def not found . . . . XNN1CN1AX9180.010.462 XNN2CN3BX9180.04.1842 XCN3CN3CX9180.00.41842 XNN2CN3CX9180.00.41842 XON4P3X90.01.25523 [ dihedraltypes ] ; ijklfuncq0cq NN2BCN4CN5HN220.058.576 NN2GCN4CN1HN220.06.6944 NN1CN2HN1HN120.050.208 CN1NN2GCN5GON120.0753.12 CN1TNN2BNN2UON120.0920.48 CN1NN2UCN3TON120.0753.12 CN2NN3GNN2GNN120.0334.72 CN2NN3ACN5NN120.0334.72 CN2NN3CN3NN120.0502.08 CN4NN2GNN3IHN320.0326.352 CN3CN3CCN8HN620.0125.52 HN2CN3CN3BNN220.0418.4 HN1HN1CN1ANN120.0-41.84 HN8CN3CN3CN820.0150.624 HR1NR1NR2CPH220.004.184 HR1NR2NR1CPH220.004.184 HR3CPH1NR1CPH120.004.184 HR3CPH1NR2CPH120.004.184 HR3NR1CPH1CPH120.004.184 HR3NR2CPH1CPH120.004.184 NR1CPH1CPH2CN7B20.005.0208 NR1CPH2CPH1CN7B20.005.0208 HN2XXNN220.08.368 HN1XXNN120.033.472 CN1XXON120.0753.12 CN1TXXON120.0753.12 CN1XXON1C20.0669.44 CN2XXNN120.0753.12 CN9XXCN3T20.0117.152 HN3BXXCN320.0125.52 HN3BXXCN3A20.0108.784 HN3BXXCN3B20.0108.784 ON1XXCN1A20.0334.72 HN3XXCN3C20.0443.504 HN6XXCN3C20.0443.504 ; Include chain topologies ; ;File 'topol_Protein_chain_A.itp' was generated ;By user: shima (1000) ;On host: linux-cbyo.site ;At date: Wed Dec 12 12:17:55 2012 ; ;This is a include topology file ; ;It was generated using program: ;pdb2gmx - VERSION 4.5.5 ; ;Command line was: ;pdb2gmx -f dimer-rotated.pdb -o dimer-processed.pdb -ter -water tip3p ; ;Force field was read from current directory
Re: Fw: [gmx-users] position restraints
1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 MG 1 MG MG 1 2 [ moleculetype ] ; molname nrexcl K 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 POT 1 K K 1 1 [ moleculetype ] ; molname nrexcl Ces 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 CES 1 Ces Ces 1 1 [ moleculetype ] ; molname nrexcl Cal 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 CAL 1 Cal Cal 1 2 [ moleculetype ] ; molname nrexcl CL 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 CLA 1 CL CL 1 -1 [ moleculetype ] ; molname nrexcl ZN 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 ZN 1 ZN ZN 1 -2 [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 POPC 238 SOL 18706 NA 615 CL 617 Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, March 26, 2013 9:55 PM Subject: Re: Fw: [gmx-users] position restraints On Tue, Mar 26, 2013 at 1:01 PM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: Have a look at processed topology file here please; I see that position restraints are brought after chain_A but not brought after chain_B. With these settings: ; Include chain topologies #ifdef POSRES #include topol_Protein_chain_A.itp #include protein_chain_A_posre.itp #endif #ifdef POSRES #include topol_Protein_chain_B.itp #include protein_chain_B_posre.itp #endif The above approach is incorrect. The inclusion of protein topologies is dependent upon using position restraints? That's certainly not right, especially if you ever want to run a simulation without restraints. The following is the correct approach: ; Include chain topologies #include topol_Protein_chain_A.itp #ifdef POSRES #include protein_chain_A_posre.itp #endif #include topol_Protein_chain_B.itp #ifdef POSRES #include protein_chain_B_posre.itp #endif Also adding define = -DPOSRES_LIPID -DPOSRES , I get this processed.top: #grompp -f nvt.mdp -c minim.gro -p topol.top -n index.ndx -o nvt.tpr -pp THIS IS THE PROCESSED TOPOLOGY: ; File 'topol.top' was generated ; By user: shima (1000) ; On host: linux-cbyo.site ; At date: Wed Dec 12 12:17:51 2012 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.5 ; ; Command line was: ; pdb2gmx -f dimer-rotated.pdb -o dimer-processed.pdb -ter -water tip3p ; ; Force field was read from current directory or a relative path - path added. ; ; Include forcefield parameters ; Conversion of CHARMM36 parameters to GROMACS format by Thomas Piggot, July 2010. ; Also added some parameters from later CHARMM27 versions, such as those for the PS headgroup. ; ; If you use these parameters please check out the forcefield.doc for papers to cite [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 1.0 ; ; Added new and changed old atomtypes and pairtypes (OSL, OSLP, HBL and CCL) - Thomas Pigot July 2010 ; [ atomtypes ] ;name at.num mass charge ptype sigma epsilon C 6 12.01100 0.51 A 0.356359487256 0.46024 CA 6 12.01100 -0.115 A 0.355005321205 0.29288 CC 6 12.01100 0.62 A 0.356359487256 0.29288 CD 6 12.01100 0.000 A 0.356359487256 0.29288 ; partial charge def not found CE1 6 12.01100 0.000 A 0.372395664183 0.284512 ; partial charge def not found . . . . X NN1 CN1A X 9 180.0 10.46 2 X NN2 CN3B X 9 180.0 4.184 2 X CN3 CN3C X 9 180.0 0.4184 2 X NN2 CN3C X 9 180.0 0.4184 2 X ON4 P3 X 9 0.0 1.2552 3 [ dihedraltypes ] ; i j k l func q0 cq NN2B CN4 CN5 HN2 2 0.0 58.576 NN2G CN4 CN1 HN2 2 0.0 6.6944 NN1 CN2 HN1 HN1 2 0.0 50.208 CN1 NN2G CN5G ON1 2 0.0 753.12 CN1T NN2B NN2U ON1 2 0.0 920.48 CN1 NN2U CN3T ON1 2 0.0 753.12 CN2 NN3G NN2G NN1 2 0.0 334.72 CN2 NN3A CN5 NN1 2 0.0 334.72 CN2 NN3 CN3 NN1 2 0.0 502.08 CN4 NN2G NN3I HN3 2 0.0 326.352 CN3 CN3C CN8 HN6 2 0.0 125.52 HN2 CN3 CN3B NN2 2 0.0 418.4 HN1 HN1 CN1A
Re: Fw: [gmx-users] position restraints
On Tue, Mar 26, 2013 at 2:20 PM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: The inclusion part was edited again in original top file. I dont know why I had written that! Sorry. But about last itp files, which you mentioned that they are created incorrectly, 1) I 'd like to know what itp file should be created? In my own, I just included the chain_B.itp file with the same numbering as the chain_A.itp file. I don't really know what that means. You should be using the files pdb2gmx gave you, at least until you understand how all of this works. You should not have to deal with anything related to restraining the protein. Hence why I've suggested that you start over. 2) One more thing, restraints for both chains are brought just one time in the processed.top file? I thought after each chain, the restraints which are included should be brought and written in processed.top file!!! They should. But what you showed makes no sense. Restraints can't correspond to atoms that don't exist and there should only ever be on [ position_restraints ] directive per [ moleculetype ]. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/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: Fw: [gmx-users] position restraints
Thanks for all your explanations. What I get as a conclusion is this: itp files are dependent to the numbering of aoms in molecule type directive and not any other things! Each posre.itp file created by genrestr should be in consistent with the molculetype numbering! Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, March 26, 2013 10:54 PM Subject: Re: Fw: [gmx-users] position restraints On Tue, Mar 26, 2013 at 2:20 PM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: The inclusion part was edited again in original top file. I dont know why I had written that! Sorry. But about last itp files, which you mentioned that they are created incorrectly, 1) I 'd like to know what itp file should be created? In my own, I just included the chain_B.itp file with the same numbering as the chain_A.itp file. I don't really know what that means. You should be using the files pdb2gmx gave you, at least until you understand how all of this works. You should not have to deal with anything related to restraining the protein. Hence why I've suggested that you start over. 2) One more thing, restraints for both chains are brought just one time in the processed.top file? I thought after each chain, the restraints which are included should be brought and written in processed.top file!!! They should. But what you showed makes no sense. Restraints can't correspond to atoms that don't exist and there should only ever be on [ position_restraints ] directive per [ moleculetype ]. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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: Fw: [gmx-users] position restraints
On Tue, Mar 26, 2013 at 2:33 PM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: Thanks for all your explanations. What I get as a conclusion is this: itp files are dependent to the numbering of aoms in molecule type directive and not any other things! Each posre.itp file created by genrestr should be in consistent with the molculetype numbering! Yes, exactly. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://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/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
FW: [gmx-users] position restraints
Thank you for your reply, I have been using [ position_restraints ], I do not know why it came out that way in the mail. I agree with you, the problem probably comes from the position the code lies in inside the .top file. I put it at the end of the file because I thought that was the way it was supposed to be done. Perhaps this is incorrect. The final lines of the .top file are: Include generic topology for ions #include ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_A 1 [ position_restraints ] 2 1 1000 0 1000 ; 3 1 1000 0 1000 ; 4 1 1000 0 1000 ; 5 1 1000 0 1000 ; 6 1 1000 0 1000 ; 7 1 1000 0 1000 ; 8 1 1000 0 1000 ; 9 1 1000 0 1000 ; Date: Thu, 3 Jun 2010 09:00:36 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] position restraints abdullah ahmed wrote: Hello, I would like to restrain my molecule to a specific position in space. I would like for certain atoms to lie on the y-axis. To do this I used the following code/lines in my .top file: [ position restraints ] This is an incorrect directive. It should be position_restraints. 2 1 1000 0 1000 ; 3 1 1000 0 1000 ; 4 1 1000 0 1000 ; 5 1 1000 0 1000 ; 6 1 1000 0 1000 ; 7 1 1000 0 1000 ; 8 1 1000 0 1000 ; 9 1 1000 0 1000 ; Unfortunately, after minimization my file contained the molecule in the same position as when the restraints were not applied. Does anyone know what I am doing wrong? Perhaps the directive name is an issue, although I think grompp should have raised a warning of some sort. Otherwise, is this block within the appropriate [moleculetype] in the topology? Is it under control of an #ifdef block that you haven't invoked in the .mdp file? -Justin Thanks in advance, Abdullah Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- 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 Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. _ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969-- 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
FW: [gmx-users] position restraints
Hi! In your previous mail you mentioned: The position restraints must belong to the [moleculetype] of the species to be restrained. Once you #include a new molecule, you start a new [moleculetype] entry and the position restraints belong to it. So I rechecked my .top file and found that [moleculetype] only occurs once. Perhaps I have misunderstood you. So I added the top file below. I did not add the contents of [atoms] [bonds] etc because I felt the mail would become unnecessarily long. ; Include forcefield parameters #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl Protein_A 3 [ atoms ] [ bonds ] [ pairs ] [ angles ] [ dihedrals ] [ dihedrals ] ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_A 1 Thanks again for your help, Abdullah Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969-- 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
