Re: [gmx-users] Top file
On 6/26/12 1:52 AM, Shima Arasteh wrote: Dear gmx users, I have a problem about the topology output of pdb2gmx. There is a formyl residue as N-terminal in my .pdb file. I know that the pdb file is correct in agreement with RCSB .pdb files. The force field I have to use is gmx ( I need to regenerate some results ), so I defined the formyl residue as a new residue in gmx force field. But when I get the output of pdb2gmx the topology shows that the N atom of the next residue has 3 H atoms ,I think It means that the formyl residue is not connected to the next residue ( here: Valine ). As a result the total charge derived by pdb2gmx is +2e and it is not correct regards to the protein structure. I don't know what is the problem? Is it related to the force field files? Did you follow all of the instructions here? http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field It also sounds like you are not setting termini properly using pdb2gmx -ter. Please provide your complete pdb2gmx command any any relevant screen output. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] Rotation aroud the z axis
Hi everybody, I use the tutorial proposed by gromacs for a membrane simulation. But when I do this and look at my protein in the membrane after the Pack the lipids around the protein step its orientation in the membrane is wrong. So my question is: how can I rotate the protein around the z axis? Bests, Eva -- 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] Rotation aroud the z axis
On 6/26/12 8:36 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I use the tutorial proposed by gromacs for a membrane simulation. But when I do this and look at my protein in the membrane after the Pack the lipids around the protein step its orientation in the membrane is wrong. So my question is: how can I rotate the protein around the z axis? editconf -rotate -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] ewald_geometry 3dc with wall gives high pressure
Zifeng Li lizife...@gmail.com Dear Gromacs users, I want to compress a polymer slab and solvate it with water to exam the interface between them. To prevent the polymer from crossing the interface along z direction, I compress it using 2 walls by moving them towards each other a little bit ( 0.5 sigma of wall atoms) and equilibrating for 50ps subsequently each time. However, the pressure is enormously high during this process. From polymer handbook, this slab should have a density of 0.98g/cm3 at 400K, 1bar. In my simulation, the density-pressure relation is : density(g/cm3) Avg. pressure(/bar) 0.45 80 0.63 245 0.86 2500 Gromacs version: 4.5.4 Here's my NVT.mdp settings: constraints = none integrator = md dt = 0.001; 1fs. nsteps = 5; total 50ps. ;neighbour searching nstlist = 10 rlist = 1.1 ns_type = grid ;coulomb coulombtype = PME rcoulomb = 1.1 ewald_geometry = 3dc ;walls(9-3 type by default) pbc = xy nwall =2 wall_atomtype =opls_139 opls_139 wall_density = 50 50 ( set is as 1g/cm3) ;vdw rvdw = 1.1 vdwtype = shift ;output control nstxout = 1000 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy = 1000 ; Generate velocites is on at 400 K. gen_vel = yes gen_temp = 400.0 gen_seed = 173529 ;temperature coupling tcoupl = v-rescale tc-grps = Polymer tau_t = 0.1 ref_t = 400 equilibrating the output of compression which has density 1.0 and run a NPT with walls, it keeps expanding to density 0.1 g/cm3 after 6ns. I doubt this high pressure issues might be caused by wall settings or ewald_geometry settings. 1. For the wall settings The density of wall (1g/cm3) is close to the density of my system (0.45~1g/cm3) and each time I run a NVT, the distance between wall and system is 0.5 sigma of wall atoms, the energy between wall and system is 4% of the total energy of my system. I don't know what's wrong or what I can check next. any problem with wall settings? Therefore, I just remove the wall and check the ewald_geometry. 2. For ewald_geometry = 3dc From the paper J.Chem.Phys.111(1999) pp3155-3162 on Ewald summation for systems with slab geometry, it requires the length of box in z direction should be at least 3 times of that in x/y direction to use this psudeo-2D PME. However, to simulate such a thick slab would be computationally expensive. Therefore, I put vacuum above and below the slab(at slab density 0.45), running a NVT without walls(10ns), the pressure goes down to some negative value near 0 and the polymer compresses itself in z direction to density avg. 0.63 along this NVT and stops shrinking. The density(0.63) is too low compared to my expectation(1.0g/cm3). However, I check the density profile and find in the middle of the slab, it has bulk density(nearly 1.0g/cm3) and the density decrease towards the interface. It seems reasonable since it has right bulk density in the middle but I lose control of pressure( along z, it is 0 because of vacuum) and density( the avg. density value is low). Is this a correct or efficient way to use 3d ewald correction when you don't want a thick slab? Thanks! --Zifeng -- 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] PBC
Hello, I have question about periodic boundary condition. Suppose if one atom is going out of the box (x axis distance is more than L/2) and it will come inside the box from other side (distance-L). Distance before the pbc should be same or it will be different from center. Thanks Nilesh -- 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] H-atoms in .hdb file
Dear gmx users, However this H-atom is defined in .hdb file of force field before, why sometimes I need to add a H-atom to the pdb on my own? Sincerely, Shima -- 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] H-atoms in .hdb file
On 6/26/12 10:25 AM, Shima Arasteh wrote: Dear gmx users, However this H-atom is defined in .hdb file of force field before, why sometimes I need to add a H-atom to the pdb on my own? A properly constructed .hdb entry eliminates the need for manual introduction of H atoms. If you aren't achieving the desired behavior, you will have to be a lot more specific about what you're doing and what you're observing. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] H-atoms in .hdb file
Thanks for you reply. As I explained befor, I need to add a formyl residue to the gmx.ff . I defined it in aminoacid.rtp file and aminoacid.n.tdb . In .rtp file: [ atoms ] C CH1 0.380 0 O O -0.380 0 [ bonds ] C O C +N [angles ] ai aj ak O C +N [ dihedrals ] O C +N +CA In .n.hdb file: [ replace ] C CH1 0.380 0 O O -0.380 0 [ bonds ] C O C +N The first residue after formyl is VAL. I know when VAL is added to FOR, a peptide bond is formed and 1 H-atom is added to the N-atom in this bonding, this H-atom is already defined in .hdb file. In my case, an error ( missing H on VAL residue) is occured, thus I decieded to add the H by hand in pdb file. Any suggestion please? Thanks so much. Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, June 26, 2012 6:58 PM Subject: Re: [gmx-users] H-atoms in .hdb file On 6/26/12 10:25 AM, Shima Arasteh wrote: Dear gmx users, However this H-atom is defined in .hdb file of force field before, why sometimes I need to add a H-atom to the pdb on my own? A properly constructed .hdb entry eliminates the need for manual introduction of H atoms. If you aren't achieving the desired behavior, you will have to be a lot more specific about what you're doing and what you're observing. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] H-atoms in .hdb file
On 6/26/12 10:44 AM, Shima Arasteh wrote: Thanks for you reply. As I explained befor, I need to add a formyl residue to the gmx.ff . I defined it in aminoacid.rtp file and aminoacid.n.tdb . In .rtp file: [ atoms ] C CH1 0.380 0 O O -0.380 0 [ bonds ] C O C +N [angles ] aiajak O C +N [ dihedrals ] OC +N +CA In .n.hdb file: [ replace ] C CH1 0.380 0 O O -0.380 0 [ bonds ] C O C +N These are the contents of a .n.tdb file, as .n.hdb files do not exist. You also do not need such modifications. If you have the formyl group in the .rtp file, and it is appropriately defined as Protein in residuetypes.dat, then all you need to do is choose None for the N-terminus of the protein. The first residue after formyl is VAL. I know when VAL is added to FOR, a peptide bond is formed and 1 H-atom is added to the N-atom in this bonding, this H-atom is already defined in .hdb file. In my case, an error ( missing H on VAL residue) is occured, thus I decieded to add the H by hand in pdb file. The error probably comes from an incorrect assignment of terminus state. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] PBC
Hey Nilesh, Distance to where? Just think of your PBC in one dimension as being on a circle. Cheers, Tsjerk On Tue, Jun 26, 2012 at 4:26 PM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: Hello, I have question about periodic boundary condition. Suppose if one atom is going out of the box (x axis distance is more than L/2) and it will come inside the box from other side (distance-L). Distance before the pbc should be same or it will be different from center. Thanks Nilesh -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] H-atoms in .hdb file
Oh, you're right. Those are the contents of the tdb file. I wrote hdb by mistake! sorry! :-) Thanks so much Justin. NOW, 1. I made an aminoacids.dat file and added FOR to other residues, as below: 49 ABU ACE AIB ALA ARG ARGN ASN ASN1 ASP ASP1 ASPH CYS CYS1 CYS2 CYSH DALA FOR GLN GLU GLUH GLY HIS HIS1 HISA HISB HISH HYP ILE LEU LYS LYSH MELEU MET MEVAL NAC NH2 PHE PHEH PHEU PHL PRO SER THR TRP TRPH TRPU TYR TYRH TYRU VAl 2. added FOR in .rtp file as before. but now, it doesn't recognize the FOR as the first residue! My protein has 25 residue but here 24 is written by gromacs. What's the problem? .dat file defined is wrong? Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, June 26, 2012 7:17 PM Subject: Re: [gmx-users] H-atoms in .hdb file On 6/26/12 10:44 AM, Shima Arasteh wrote: Thanks for you reply. As I explained befor, I need to add a formyl residue to the gmx.ff . I defined it in aminoacid.rtp file and aminoacid.n.tdb . In .rtp file: [ atoms ] C CH1 0.380 0 O O -0.380 0 [ bonds ] C O C +N [angles ] ai aj ak O C +N [ dihedrals ] O C +N +CA In .n.hdb file: [ replace ] C CH1 0.380 0 O O -0.380 0 [ bonds ] C O C +N These are the contents of a .n.tdb file, as .n.hdb files do not exist. You also do not need such modifications. If you have the formyl group in the .rtp file, and it is appropriately defined as Protein in residuetypes.dat, then all you need to do is choose None for the N-terminus of the protein. The first residue after formyl is VAL. I know when VAL is added to FOR, a peptide bond is formed and 1 H-atom is added to the N-atom in this bonding, this H-atom is already defined in .hdb file. In my case, an error ( missing H on VAL residue) is occured, thus I decieded to add the H by hand in pdb file. The error probably comes from an incorrect assignment of terminus state. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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-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] H-atoms in .hdb file
I tried again as below: 1. defined FOR in .rtp file 2. defined FOR in aminoacids.dat file. 3. chose NH2 as N-Terminal and then got this topology for FOR and VAL: ; residue 0 FOR rtp FOR q 0.0 1 CH1 0 FOR C 1 0.38 13.019 ; qtot 0.38 2 O 0 FOR O 1 -0.38 15.9994 ; qtot 0 ; residue 1 VAL rtp VAL q 0.0 3 NL 1 VAL N 2 -0.83 14.0067 ; qtot -0.83 4 H 1 VAL H1 2 0.415 1.008 ; qtot -0.415 5 H 1 VAL H2 2 0.415 1.008 ; qtot 0 6 CH1 1 VAL CA 3 0 13.019 ; qtot 0 7 CH1 1 VAL CB 4 0 13.019 ; qtot 0 8 CH3 1 VAL CG1 5 0 15.035 ; qtot 0 9 CH3 1 VAL CG2 6 0 15.035 ; qtot 0 10 C 1 VAL C 7 0.38 12.011 ; qtot 0.38 11 O 1 VAL O 7 -0.38 15.9994 ; qtot 0 I guess the topology is correct. Isn't it? Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, June 26, 2012 7:17 PM Subject: Re: [gmx-users] H-atoms in .hdb file On 6/26/12 10:44 AM, Shima Arasteh wrote: Thanks for you reply. As I explained befor, I need to add a formyl residue to the gmx.ff . I defined it in aminoacid.rtp file and aminoacid.n.tdb . In .rtp file: [ atoms ] C CH1 0.380 0 O O -0.380 0 [ bonds ] C O C +N [angles ] ai aj ak O C +N [ dihedrals ] O C +N +CA In .n.hdb file: [ replace ] C CH1 0.380 0 O O -0.380 0 [ bonds ] C O C +N These are the contents of a .n.tdb file, as .n.hdb files do not exist. You also do not need such modifications. If you have the formyl group in the .rtp file, and it is appropriately defined as Protein in residuetypes.dat, then all you need to do is choose None for the N-terminus of the protein. The first residue after formyl is VAL. I know when VAL is added to FOR, a peptide bond is formed and 1 H-atom is added to the N-atom in this bonding, this H-atom is already defined in .hdb file. In my case, an error ( missing H on VAL residue) is occured, thus I decieded to add the H by hand in pdb file. The error probably comes from an incorrect assignment of terminus state. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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-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] H-atoms in .hdb file
On 6/26/12 11:36 AM, Shima Arasteh wrote: I tried again as below: 1. defined FOR in .rtp file 2. defined FOR in aminoacids.dat file. 3. chose NH2 as N-Terminal and then got this topology for FOR and VAL: ; residue 0 FOR rtp FOR q 0.0 1CH1 0FOR C 1 0.38 13.019 ; qtot 0.38 2 O 0FOR O 1 -0.3815.9994 ; qtot 0 ; residue 1 VAL rtp VAL q 0.0 3 NL 1VAL N 2 -0.8314.0067 ; qtot -0.83 4 H 1VAL H1 2 0.415 1.008 ; qtot -0.415 5 H 1VAL H2 2 0.415 1.008 ; qtot 0 6CH1 1VAL CA 3 0 13.019 ; qtot 0 7CH1 1VAL CB 4 0 13.019 ; qtot 0 8CH3 1VALCG1 5 0 15.035 ; qtot 0 9CH3 1VALCG2 6 0 15.035 ; qtot 0 10 C 1VAL C 7 0.38 12.011 ; qtot 0.38 11 O 1VAL O 7 -0.3815.9994 ; qtot 0 I guess the topology is correct. Isn't it? No, it isn't. An NH2 terminal says the N-terminus of VAL is a neutral amine. You should choose None for the terminus. The formyl group occupies the N-terminus as would another amino acid in a peptide bond, but there is no special protonation of FOR. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] H-atoms in .hdb file
OK, but when I chose none, it gives me a fatal error ( dangling bond! ). A new problem! So how do I solve it? Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, June 26, 2012 8:09 PM Subject: Re: [gmx-users] H-atoms in .hdb file On 6/26/12 11:36 AM, Shima Arasteh wrote: I tried again as below: 1. defined FOR in .rtp file 2. defined FOR in aminoacids.dat file. 3. chose NH2 as N-Terminal and then got this topology for FOR and VAL: ; residue 0 FOR rtp FOR q 0.0 1 CH1 0 FOR C 1 0.38 13.019 ; qtot 0.38 2 O 0 FOR O 1 -0.38 15.9994 ; qtot 0 ; residue 1 VAL rtp VAL q 0.0 3 NL 1 VAL N 2 -0.83 14.0067 ; qtot -0.83 4 H 1 VAL H1 2 0.415 1.008 ; qtot -0.415 5 H 1 VAL H2 2 0.415 1.008 ; qtot 0 6 CH1 1 VAL CA 3 0 13.019 ; qtot 0 7 CH1 1 VAL CB 4 0 13.019 ; qtot 0 8 CH3 1 VAL CG1 5 0 15.035 ; qtot 0 9 CH3 1 VAL CG2 6 0 15.035 ; qtot 0 10 C 1 VAL C 7 0.38 12.011 ; qtot 0.38 11 O 1 VAL O 7 -0.38 15.9994 ; qtot 0 I guess the topology is correct. Isn't it? No, it isn't. An NH2 terminal says the N-terminus of VAL is a neutral amine. You should choose None for the terminus. The formyl group occupies the N-terminus as would another amino acid in a peptide bond, but there is no special protonation of FOR. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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-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] H-atoms in .hdb file
On 6/26/12 11:47 AM, Shima Arasteh wrote: OK, but when I chose none, it gives me a fatal error ( dangling bond! ). A new problem! So how do I solve it? Dangling bond errors were introduced as part of the output in Gromacs 4.5. The aminoacids.dat file was only used by older (4.0.x and earlier) versions of Gromacs. You need to be modifying residuetypes.dat to indicate that FOR is a Protein residue so that the chain is continuous with respect to its content type. http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] Lipid-protein simulation....
Hi Gromacs Friends, I completed Justin-Lipid Tutorial. I plan to simulate protein-lipid system to study protein-lipid interaction. My Query is like 1. I plan to use DPPC (128) lipid from Tieleman Website. I removed its periodicity as per tutorial instruction.. I found that I need the z box Dimension more than 6.59650. ( I not Change x-y box Dimension , As it affect the equilibrated DPPC layer). So with help of editconf command I changed the Z box Dimension to 8.00 while x and y are same . Is these process is right or any good suggestion in my work-flow ??? 2. I wish to put lipid membrane away from protein ( Protein is not embedded in lipid ). Should I use InflateGro?? Should I use Strong position restrain during Energy minimisation??? please give me valuable Guidance With Best Wishes and regards Rama -- 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: Lipid-protein simulation....
On Tue, Jun 26, 2012 at 9:32 PM, rama david ramadavidgr...@gmail.com wrote: Hi Gromacs Friends, I completed Justin-Lipid Tutorial. I plan to simulate protein-lipid system to study protein-lipid interaction. My Query is like 1. I plan to use DPPC (128) lipid from Tieleman Website. I removed its periodicity as per tutorial instruction.. I found that I need the z box Dimension more than 6.59650. ( I not Change x-y box Dimension , As it affect the equilibrated DPPC layer I deleted SOL molecule from DPPC layer, I plan to solvate system after catenation of lipid and protein gro file). So with help of editconf command I changed the Z box Dimension to 8.00 while x and y are same . Is these process is right or any good suggestion in my work-flow ??? 2. I wish to put lipid membrane away from protein ( Protein is not embedded in lipid ). Should I use InflateGro?? Should I use Strong position restrain during Energy minimisation??? please give me valuable Guidance With Best Wishes and regards Rama -- 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] number of gauche - trans transitions with CHARMM36 and AMBER force fields
Dear all, I would like to compute the number of gauche -- trans transitions (per ns) for for several alkanes. I know that I can use g_angle with -ot flag. But in the manual it is stated that this command works only for dihedrals with multiplicity 3. In CHARMM36 force field, for example, the dihedrals parameters have the following form: CTL2CTL2CTL2CTL39 0.000.6778082 ; New CTL2CTL2CTL2CTL39 180.00 0.1966483 ; New CTL2CTL2CTL2CTL39 0.000.43932 4 ; New CTL2CTL2CTL2CTL39 0.000.7405685 ; New CTL2CTL2CTL2CTL29 0.000.4225842 ; New CTL2CTL2CTL2CTL29 180.00 0.5941283 ; New CTL2CTL2CTL2CTL29 0.000.3096164 ; New CTL2CTL2CTL2CTL29 0.000.4058485 ; New So it is possible to use the g_angle functionality with this force field ? Probably I can comment the lines where the angle multiplicity is not equal tp 3 and regenerate a tpr file and use it with g_angle, right ? Stephane -- 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] Lipid-protein simulation....
On 6/26/12 12:02 PM, rama david wrote: Hi Gromacs Friends, I completed Justin-Lipid Tutorial. I plan to simulate protein-lipid system to study protein-lipid interaction. My Query is like 1. I plan to use DPPC (128) lipid from Tieleman Website. I removed its periodicity as per tutorial instruction.. I found that I need the z box Dimension more than 6.59650. ( I not Change x-y box Dimension , As it affect the equilibrated DPPC layer). So with help of editconf command I changed the Z box Dimension to 8.00 while x and y are same . Is these process is right or any good suggestion in my work-flow ??? Changing the box dimensions to accommodate new species is fine. By default, if you haven't used the -center option of editconf, the coordinates are position such that the solute is centered within the box. This may or may not be what you want. Check out the workflow and tips suggested here: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/03_tricks.html 2. I wish to put lipid membrane away from protein ( Protein is not embedded in lipid ). Should I use InflateGro?? Should I use Strong position restrain during Energy minimisation??? The purpose of InflateGRO is to pack lipids around a protein. If you don't need to embed the protein in the membrane, there is no point to using InflateGRO, or programs like g_membed. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] What's the effect of non-neotron charge group?
Dear Gromacs users, I use gromacs version 4.5.4 and build residue of my own polymers which has a ester group (COOR). From aminoacids.atp database, I found the partial charge of each atom, where the carbolic group COO- is not neutron and has to be neutralized by a methyl group. Should I consider the ester as one neutral group or split it into two groups? Here's some exploration I have done: 1. Should consider them as one group. Based on the fact that Gromacs consider a charge group to be a moving particle so that if I make a non-neutral charge group ( i.e., COO- , methyl connected to it as two charge groups), the total charge of a verlet list might not be 0 if these two groups are not included in a list at the same time. 2. Should split into two groups. First, on Gromacs website, it is said the charge group usually includes 4 or less atoms. Considering this, it seems that I have to split the ester group into two groups. Second, in aminoacids.rtp file, I find some aminoacids, like Asn, which do have a non-neutral charge group. Would this really make a difference? Thanks in advance, -Zifeng -- 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] What does --enable-fahcore mean?
Hi, all, I am wondering what the --enable-fahcore option of configure means. I got the explanation from configure --help of create a library with mdrun functionality, while it is not very clear to me. Best Regards, Kai -- 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] What does --enable-fahcore mean?
It only matters for running on Folding@Home. For other users of gromacs, it doesn't do anything. On Tue, Jun 26, 2012 at 3:50 PM, Bao Kai paeanb...@gmail.com wrote: Hi, all, I am wondering what the --enable-fahcore option of configure means. I got the explanation from configure --help of create a library with mdrun functionality, while it is not very clear to me. Best Regards, Kai -- 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
[gmx-users] wrong distances with g_dist
Hi, I try to calculate distance between two atoms with g_dist. Somewhat I get distance lower than actual. Here there are coordinates of the two atoms (PDB format) ATOM702 CZ ARG X 45 5.930 9.230 41.740 0.00 0.00 ATOM 2751 CA PHE X 177 41.710 45.000 27.180 0.00 0.00 And the distance I get from g_dist is 4.6260725 nm while the actual is 5.265 nm. What the problem can be? Dmytro -- 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] Unusual g_order with CHARMM36
Dear Gmx users, anyone which used the CHARMM36 (available for downloading in the Gromacs website) for simulating a POPC, POPE or whatever POxx membrane in Gromacs has found an unusual behavior in the Oleyl chain when it comes to the deuterium order parameter (Scd)? Let me explain a little further. I'm running a system with parameters consistent to those in [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) and discussed in this thread: http://www.mail-archive.com/gmx-users@gromacs.org/msg34641.html Now, membrane thickness, area per lipid and the order parameter for the the palmitoyl chains are consistent with a liquid-crystal phase. Most carbons for the oleyl chains are in agreement with the literature, with notable exception for the central part of the plot [C27,C28, C29], when the values form a w shape, instead of the characteristic v shape. I ran more than one system, each with distinct lipid composition, they all give me these similar results. If anyone has some ideas, I'd be grateful. Thank you, Ricardo. -- 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] Atoms get frozen with Nose Hoover thermostat with Parrinello-Rahman barostat for a system of an ion of charge +2 in flexible water molecules
Dear Gromacs users, I am having a very strange problem with Nose Hoover thermostat with Parrinello-Rahman barostat NPT simulations for a system of an ion of charge +2 in flexible water molecules. Flexible water is taken from J. Chem. Phys. 124, 024503 (2006); http://dx.doi.org/10.1063/1.2136877. The ion is [UO2]2+ with charge on U=2.5 and each O has -0.25. Atoms very soon get frozen after the simulation starts and they remain frozen, they do not move at all. Only simulation box oscillates, which causes atoms to oscillate little bit but they do not move at all. Pressure, temperature etc. all get messed up. Here is some output from g_energy: Statistics over 41 steps [ 0. through 400. ps ], 3 data sets All statistics are over 40001 points Energy Average Err.Est. RMSD Tot-Drift --- Potential -23648.5 202891.04 -117.711 (kJ/mol) Temperature 306.6840.1108.192 -0.566776 (K) Pressure538.6254.489041.8 79.925 (bar) I am using this Nose Hoover thermostat with Parrinello-Rahman barostat after a well equilibration configuration obtained with Berendsen's thermostat and barostat. This problem is happening only when Parrinello-Rahman barostat used with Nose Hoover thermostat. I also noted the following observations: If I change either one of the thermostat or barostat with Berendsen, frozen problem disappears. If I change flexible water to rigid water, problem disappears. If my system has no ion, no problem happens. If I play with cut offs, rlist, then also sometimes problem disappears. The problem is independent on the size of box and number of water molecules. As expected, Diffusion constant is very close to zero. Here is my input MDP file: integrator = md dt = 0.001 tinit = 0 nsteps = 40 nstcomm = 10 pbc = xyz ;constraint_algorithm= lincs ;constraints = all-bonds continuation= yes ; continuing from equilibrated NPT nstxout = 200 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy= 2000 nstxtcout= 0 xtc-precision= 1000 nstlist = 10 ns_type = grid rlist= 1.1 coulombtype = PME_switch rcoulomb_switch = 0.6 rcoulomb = 0.9 vdw-type = switch rvdw-switch = 0.6 rvdw = 0.9 DispCorr= EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-6 optimize_fft= yes tcoupl = nose-hoover tc-grps = System tau_t = 2 ref_t = 298.15 pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure (in bar) compressibility = 4.5e-5; isothermal compressibility, bar^-1 gen_vel = no Any help will be highly appreciated. Please let me know if someone needs any additional information to solve this issue. Thanks, Surya Prakash Tiwari -- 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] Fwd: About Justin Lipid-protein simulation tutorial
Hi Gromacs Friends, I am doing Justin-lipid tutorialer http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html In these the npt.mdp has a parameter refcoord_scaling = com Why these parameter is introduced in NPT of lipid-protein simulation and not use in Lysozyme in water simulation ??? Please give the detail on why to use these parameter?? Thank you in advance With best Wishes and Regards, Rama -- 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
