[gmx-users] (no subject)
Dear Justin/Mark, I would like to have a private course about Gromacs in Holland. Is there such a facility for this? Who should I talk with? Or is there a workshop in near future? best wishes -- 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] (no subject)
Dear users, How can we fix the position of some atoms? best wishes trevor -- 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] CNT
Dear Justin, Regarding our previous discussion under CNT topic, you want to know exactly what I did to define C-C interaction. I have summarized it below. 1. I copied oplsaa.ff folder in my working directory 2. I added following lines to atomname2type.n2t Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 4C 0.142 C 0.142 C 0.142 C 0.142 Copls_9980 12.011 5C 0.142 C 0.142 C 0.142 C 0.142 C 0.142 3. I added those to atomtypes.atp opls_995 12.01100 ; opls_996 12.01100 ; opls_997 12.01100 ; opls_998 12.01100 ; 4. I added those to ffbonded.itp [ bondtypes ] C C1 0.14210 478900 [ angletypes ] C CC 1 120.000 562.2 [ dihedraltypes ] 5. I constructed .top file for CNT with the following, then I converted it into .itp by vi editor g_x2top -f cnt.gro -o cnt.top -nopairs -nexcl 5 6. By pdb2gmx, I obtained .top for peptide then I converted it into .itp 7. I combined CNT and peptide's pdbs in pymol and saved. 8. I wrote a .top file given below, ; ; File 'topol.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Mon Jan 10 02:51:19 2011 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.3 ; ; Command line was: ; pdb2gmx -ignh -f vpgvg10.pdb ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include forcefield.itp ; Include topology for CNT #include cnt.itp ; Include topology for UW1 #include uw1.itp ; Include water topology #include spc.itp [ system ] ; Name Protein and CNT in water [ molecules ] ; Compound#mols Protein 1 CNT 1 SOL 4019 9. When I make grompp for minimization it givea me the following error WARNING 1 [file ffbonded.itp, line 2703]: Overriding Bond parameters. old: 0.151 292880 0.151 292880 new: C C1 0.14210 478900 ERROR 1 [file ffbonded.itp, line 2707]: Not enough parameters Generated 334153 of the 334153 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 334153 of the 334153 1-4 parameter combinations --- Program grompp, VERSION 4.5.3 Source code file: toppush.c, line: 1166 Fatal error: Atomtype opls_996 not found That is all what I exactly did. Is anything wrong or missing? best wishes trevor -- 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] CNT
Hi Justin, I added lines to ffnonbonded.itp. It resulted in following error. It has some warnings and an error. I am interested in error. After that I will look at the warnings. In which file we may have an error? It is not specified. best wishes trevor Generated 335790 of the 335790 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 335790 of the 335790 1-4 parameter combinations Excluding 5 bonded neighbours molecule type 'ICE' Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' Warning: atom name 170 in topol.top and final2.gro does not match (H1 - CA) Warning: atom name 171 in topol.top and final2.gro does not match (H2 - C) Warning: atom name 172 in topol.top and final2.gro does not match (H3 - O) Warning: atom name 173 in topol.top and final2.gro does not match (CA - CB) Warning: atom name 174 in topol.top and final2.gro does not match (HA - CG) Warning: atom name 175 in topol.top and final2.gro does not match (CB - CD1) Warning: atom name 176 in topol.top and final2.gro does not match (HB1 - CD2) Warning: atom name 177 in topol.top and final2.gro does not match (HB2 - HA) Warning: atom name 178 in topol.top and final2.gro does not match (CG - HB1) Warning: atom name 179 in topol.top and final2.gro does not match (HG - HB2) Warning: atom name 180 in topol.top and final2.gro does not match (CD1 - HG) Warning: atom name 184 in topol.top and final2.gro does not match (CD2 - HD21) Warning: atom name 185 in topol.top and final2.gro does not match (HD21 - HD22) Warning: atom name 186 in topol.top and final2.gro does not match (HD22 - HD23) Warning: atom name 187 in topol.top and final2.gro does not match (HD23 - H1) Warning: atom name 188 in topol.top and final2.gro does not match (C - H2) Warning: atom name 189 in topol.top and final2.gro does not match (O - N) Warning: atom name 190 in topol.top and final2.gro does not match (N - CA) Warning: atom name 191 in topol.top and final2.gro does not match (H - C) Warning: atom name 192 in topol.top and final2.gro does not match (CA - O) (more than 20 non-matching atom names) WARNING 2 [file topol.top, line 39]: 184 non-matching atom names atom names from topol.top will be used atom names from final2.gro will be ignored There were 2 warnings --- Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 1356 Fatal error: There was 1 error in input file(s) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re:Re: CNT
Dear Mark, Do you mean I will obtain 2 seperate .itp files for CNT and peptide. And I already have spc.itp. Then I will write a short .top file which only consists of include files. Is that all what I will do? In addition, I think I should combine pdbs od CNT and peptide by pymol,VMD etc. best wishes trevor On 18/01/2011 10:25 AM, trevor brown wrote: Dear friends, I have constructed a .top file for a CNT by g_x2top. to do this I have added C-C interactions in .n2t file and also related ff in .atomtypes.atp. I have also a .top file for a peptide by pdb2gmx. My aim is to construct a simulation system in which I want to see the adsorption. I don't know the next steps, could you guide me for further steps? You need to end up with a .top file that has the logical structure of #include force field files #include CNT.itp #include peptide.itp #include solvent.itp [molecules] CNT 1 Peptide 1 SOL 1 and a coordinate file whose molecules are ordered exactly as in the above field, and whose atoms within molecules are ordered exactly as in the [atoms] fields in the .itp file. Your molecule names must match those given in the .itp files. See the examples in section 5.7.1-5.7.3 of the manual. Mark My second question; I have .gro and .tp files for both CNT and peptide, do I need any other files such as .itp or .ndx? Last question: Do you have such a tutorial? best wishes trevor -- 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] CNT
Dear friends, I have the following topology for system including CNT+peptide+water When I grompp for minimization, I got the following error. How can I solve it? best wishes trevor WARNING 1 [file ffbonded.itp, line 2703]: Overriding Bond parameters. old: 0.151 292880 0.151 292880 new: C C 1 0.14210478900 ERROR 1 [file ffbonded.itp, line 2709]: Not enough parameters --- Program grompp, VERSION 4.5.3 Source code file: topio.c, line: 675 Fatal error: Syntax error - File forcefield.itp, line 20 Last line read: '1 3 yes 0.5 0.5' Found a second defaults directive. TOPOLOGY ; Include forcefield parameters #include oplsaa.ff/forcefield.itp ; Include topology for CNT #include cnt.itp ; Include topology for UW1 #include uw1.itp ; Include water topology #include oplsaa.ff/spc.itp [ system ] ; Name Protein and CNT in water [ molecules ] ; Compound#mols Protein 1 CNT 1 SOL 4019 -- 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] grompp error
Dear users, I have the following error with grompp before minimization. I defined opls_996 for C atom by myself. Any suggetions to solve it? best trevor WARNING 1 [file ffbonded.itp, line 2703]: Overriding Bond parameters. old: 0.151 292880 0.151 292880 new: C C 1 0.14210478900 ERROR 1 [file ffbonded.itp, line 2709]: Not enough parameters Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations --- Program grompp, VERSION 4.5.3 Source code file: toppush.c, line: 1166 Fatal error: Atomtype opls_996 not found -- 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] CNT
Dear friends, I have constructed a .top file for a CNT by g_x2top. to do this I have added C-C interactions in .n2t file and also related ff in .atomtypes.atp. I have also a .top file for a peptide by pdb2gmx. My aim is to construct a simulation system in which I want to see the adsorption. I don't know the next steps, could you guide me for further steps? My second question; I have .gro and .tp files for both CNT and peptide, do I need any other files such as .itp or .ndx? Last question: Do you have such a tutorial? best wishes trevor -- 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] CNT
Dear users, In Gromacs 4.5.3, atom types are defined in /share/top/oplsaa.ff/atomtypes.atp. The corresponding bonds for diffrent atopm pairs are described as between opls_001 and opls_965. I have a CNT, I need C-C intereaction, which one should I choose? Second question; where can I find info about opls_XXX? trevor -- 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] topoloy for CNT
Dear friends, My aim is to establish a topology for a CNT. My commands and the error are below. Does anyone tell me what I should do? trevor COMMANDS: editconf -f cnt.pdb -o box.gro -c -box 8.0 8.0 8.0 genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro g_x2top -f box.gro -o box.top -pbc -nopairs -name cnt1 -nexcl 5 ERROR: . . . Can not find forcefield for atom C-1498 with 2 bonds Can not find forcefield for atom C-1499 with 2 bonds Can not find forcefield for atom C-1500 with 2 bonds --- Program g_x2top, VERSION 4.5.3 Source code file: g_x2top.c, line: 206 Fatal error: Could only find a forcefield type for 0 out of 1500 atoms -- 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] Atomype HW not found
Dear all, I have Atomype HW not found error when I use gromos43a1 in water at the end of grompp. However there is no error if I just change the forcefield to oplsaa. My topology file follows. Any suggestions? trevor ; Include forcefield parameters #include gromos43a1.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Protein_chain_A 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 4 CYS rtp CYS2 q +1.0 1 NL 4CYS N 1 0.12914.0067 ; qtot 0.129 2 H 4CYS H1 1 0.248 1.008 ; qtot 0.377 3 H 4CYS H2 1 0.248 1.008 ; qtot 0.625 4 H 4CYS H3 1 0.248 1.008 ; qtot 0.873 5CH1 4CYS CA 2 0.127 13.019 ; qtot 1 6CH2 4CYS CB 2 0 14.027 ; qtot 1 7 S 4CYS SG 2 0 32.06 ; qtot 1 8 C 4CYS C 3 0.38 12.011 ; qtot 1.38 9 O 4CYS O 3 -0.3815.9994 ; qtot 1 ; residue 5 ILE rtp ILE q 0.0 10 N 5ILE N 4 -0.2814.0067 ; qtot 0.72 11 H 5ILE H 4 0.28 1.008 ; qtot 1 . . . . .. ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include gromos43a1.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include gromos43a1.ff/ions.itp [ system ] ; Name OMEGA-AGA-IVB in water [ molecules ] ; Compound#mols Protein_chain_A 1 SOL 3177 -- 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] Atomtpe HW not found-2
Dear friends, My run commands are below. It works without any error. However if I add -water tip3p at the end of pdg2gmx ... line it causes an error (Atomtpe HW not found) at grompp time. Could anyone explain the difference? trevor pdb2gmx -ignh -f XXX.pdb -o fws.gro -p fws.top editconf -f fws.gro -bt dodecahedron -d 1.0 editconf -f out.gro -o fws_ctr.gro -center 1.7 1.7 1.2 genbox -cp fws_ctr.gro -cs spc216.gro -o fws_b4em.gro -p fws.top -- 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] Water models usage info
Dear Mark, Thank you for your reply which solved my problem. I want to add something for all gmx-users. I looked at the force field folders in share/top in which possible usable water models for each force field are listed in watermodels.dat files. If you want to use a different model that is not included in the list, look at the pdb2gmx title at the end of the manual. trevor On 10/01/2011 2:41 AM, trevor brown wrote: Dear friends, My run commands are below. It works without any error. However if I add -water tip3p at the end of pdg2gmx ... line it causes an error (Atomtpe HW not found) at grompp time. Could anyone explain the difference? trevor pdb2gmx -ignh -f XXX.pdb -o fws.gro -p fws.top editconf -f fws.gro -bt dodecahedron -d 1.0 editconf -f out.gro -o fws_ctr.gro -center 1.7 1.7 1.2 genbox -cp fws_ctr.gro -cs spc216.gro -o fws_b4em.gro -p fws.top Not all water models are intended to go with all force fields. G43a1 does not define the HW atom type used for TIP3P water, possibly by Berk's design :-). I don't remember whether it's reasonable to want to use TIP3P with the GROMOS forcefields, but presumably SPC water will work with them. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
