[gmx-users] Re: problems running grompp with protein-ligand complex
Dear Fabricio, It's not only you who is confused here... So, I will try to help the best I can and sorry if I ask you redundant questions you've likely answer before. It happens that I read GMX mailing list in digest mode. BTW, when replying gmx list, cc to my email (alanwilter _at gmail . com) and so you can have a prompt reply. AFAIU, you have a protetin (receptor.itp?) and a ligand, right? And your ligand is not covalently bond to the protein, isn't it? If so, have you see this?: http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs Have you seen this note?: *NB(1):* #include "Ligand.itp" has to be inserted right after ffamber**.itp line and before Protein_*.itp line in *Complex.top*. It seems that you missing the difference between *.top and *.itp files. So, as Justin said, read chapter 5 of GMX manual. Another alternative, if you pretty familiar to AMBER and tleap is to build your system there and once you have your prmtop and inpcrd files, use acpypi to convert them to GMX files and put run EM and MD. If all I am saying here is still not helping, consider to send me your input PDB file (protein and complex) and let me run it here. Just one more thing, would you mind where are you from and what's your institute? Many thanks in advance, Alan On Thu, Dec 4, 2008 at 04:01, <[EMAIL PROTECTED]> wrote: > > I am working with a system using ffamber99 forcefield and trying to > set up a ligand protein complex system. I have encountered some > problems with grompp now. > In my past email, the problem was that : > Fatal error: Found a second > defaults directive, file "ligand.itp", line 5. Then the following > solution was given: > > " You have to combine all atomtypes into one file something like > > filename ff_atomtypes.itp > > #define FF_ATOMTYPES > > [ defaults ] > ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ > 1 2 yes 0.5 0.8333 > > > [ atomtypes ] > ; namemass chargeptype sigma > epsilon > > S 0. 0. A 3.56359e-01 1.04600e+00 > CC 0. 0. A 3.39967e-01 3.59824e-01 > HO 0. 0. A 0.0e+00 0.0e+00 > N3 0. 0. A 3.25000e-01 7.11280e-01 > all atom types from amber force field 99 and also from your ligand (check > if > parameters are ok). > > > delete atomtypes and defaults entry in your ligand.itp > > load in your .top > > #include "ff_atomtypes.itp" > > #include "receptor.itp" > #include "ligand.itp" > " > I tried to do this and ended up with the following .top file: > > ; 15d-pgj2_GMX.top created by acpypi on Wed Dec 3 14:10:55 2008 > > [ defaults ] > ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ > 1 2 yes 0.5 0.8333 > > ; Include 15d-pgj2_GMX.itp topology > #include "15d-pgj2_GMX.itp" > > [ system ] > 15d-pgj2 > > [ molecules ] > ; Compoundnmols > 15d-pgj2 1 > > And all the atomtypes are in the 15d-pgj2_GMX.itp, which is too big to > put here. But is present in past posts. > Ok, so no grompp tells me the same error it did before. Fatal error: > Found a second defaults directive, file "15d-pgj2_GMX.top" > > When I substitute the 15d-pgj2_GMX.top for the 15d-pgj2_GMX.itp in my > protein.top grompp gives out the following error: > > Fatal error:No such moleculetype PJ2 > > Now I am quite confused and would like some advice on the matter. > Thank you > Fabrício Bracht > > -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<< ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: problems running grompp with protein-ligand complex
Hi, On Tuesday, 2. December 2008, Ragnarok sdf wrote: > Hello. I will try now to send part of my itp file and if another part > of the file is needed I will send it if requested. > Below are the emails that were already sent regarding my problem. > I hope I have not caused any incovenience. > Fabrício Bracht You have to combine all atomtypes into one file something like filename ff_atomtypes.itp #define FF_ATOMTYPES [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ; namemass chargeptype sigma epsilon S 0. 0. A 3.56359e-01 1.04600e+00 CC 0. 0. A 3.39967e-01 3.59824e-01 HO 0. 0. A 0.0e+00 0.0e+00 N3 0. 0. A 3.25000e-01 7.11280e-01 all atom types from amber force field 99 and also from your ligand (check if parameters are ok). delete atomtypes and defaults entry in your ligand.itp load in your .top #include "ff_atomtypes.itp" #include "receptor.itp" #include "ligand.itp" ... greetings, Florian > > " I am working with a protein-ligand complex in gromacs with ffamber99 > forcefield. I was able to generate the topology file for my ligand > with acpypi. Was also able to insert the ligand coordinates into my > protein's coordinate file. Was also able to generate the water box > with genbox. The number of molecules all match, the ligand coordinates > are still there but grompp tells me that: > Fatal error: Found a second defaults directive, file "ligand.itp", line 5 > I've checked wikigromacs, but the solution given there, to simply > erase the second default line does not suit me here. Once I do this, i > mean, go to my ligand.itp file and put a ; before my default section, > grompp does not recognize anymore that my ligand is there and gives > out another error line. > I would like some advice on the matter if possible. > Thank you in advance > Fabrício Bracht > > >Well, it's not like grompp is recognizing you have a ligand there > >right now, is it? grompp doesn't reach the point where it realizes you > >don't seem to have a ligand. It seems there's something wrong with the > >topology. Better post ligand.itp, like Justin suggests, and also give > >the error which occurs when you do comment out the defaults line in > >the ligand topology. > > > >Cheers, > > > >Tsjerk " > > Now, the actual itp file. > > ; M_E.top created by acpypi on Wed Nov 26 18:00:37 2008 > > [ defaults ] > ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ > 1 2 yes 0.5 0.8333 > > [ atomtypes ] > ;name bond_type mass charge ptype sigma epsilon > Amb oo 0.0 0.0 A 2.95992e-01 > 8.78640e-01 ; 1.66 0.2100 > cc 0.0 0.0 A 3.39967e-01 > 3.59824e-01 ; 1.91 0.0860 > oh oh 0.0 0.0 A 3.06647e-01 > 8.80314e-01 ; 1.72 0.2104 > ho ho 0.0 0.0 A 0.0e+00 > 0.0e+00 ; 0.00 0. > c3 c3 0.0 0.0 A 3.39967e-01 > 4.57730e-01 ; 1.91 0.1094 > hc hc 0.0 0.0 A 2.64953e-01 > 6.56888e-02 ; 1.49 0.0157 > c2 c2 0.0 0.0 A 3.39967e-01 > 3.59824e-01 ; 1.91 0.0860 > ha ha 0.0 0.0 A 2.59964e-01 > 6.27600e-02 ; 1.46 0.0150 > ce ce 0.0 0.0 A 3.39967e-01 > 3.59824e-01 ; 1.91 0.0860 > cf cf 0.0 0.0 A 3.39967e-01 > 3.59824e-01 ; 1.91 0.0860 > > [ moleculetype ] > ;namenrexcl > M_E 3 > > [ atoms ] > ; nr type resi res atom cgnr charge mass typeB > chargeB 1o 1M_E O491 -0.55230 16.0 ; qtot > -0.552 2c 1M_E C482 0.63200 12.01000 ; qtot > 0.080 3 oh 1M_E O503 -0.60900 16.0 ; qtot > -0.529 4 ho 1M_E H514 0.44690 1.00800 ; qtot > -0.082 5 c3 1M_E C455 -0.12590 12.01000 ; qtot > -0.208 6 hc 1M_E H466 0.08080 1.00800 ; qtot > -0.127 7 hc 1M_E H477 0.08110 1.00800 ; qtot > -0.046 8 c3 1M_E C428 -0.07210 12.01000 ; qtot > -0.118 9 hc 1M_E H439 0.06640 1.00800 ; qtot > -0.052 10 hc 1M_E H44 10 0.05040 1.00800 ; qtot > -0.002 11 c3 1M_E C39 11 -0.05170 12.01000 ; qtot > -0.053 12 hc 1M_E H40 12 0.04490 1.00800 ; qtot > -0.008 13 hc 1M_E H41 13 0.05410 1.00800 ; qtot > 0.046 14 c2 1M_E C37 14 -0.16730 12.01000 ; qtot > -0.122 15 ha 1M_E H38 15 0.11950 1.00800 ; qtot > -0.002 16 c2 1M_E C35
[gmx-users] Re: problems running grompp with protein-ligand complex
Hello. I will try now to send part of my itp file and if another part of the file is needed I will send it if requested. Below are the emails that were already sent regarding my problem. I hope I have not caused any incovenience. Fabrício Bracht " I am working with a protein-ligand complex in gromacs with ffamber99 forcefield. I was able to generate the topology file for my ligand with acpypi. Was also able to insert the ligand coordinates into my protein's coordinate file. Was also able to generate the water box with genbox. The number of molecules all match, the ligand coordinates are still there but grompp tells me that: Fatal error: Found a second defaults directive, file "ligand.itp", line 5 I've checked wikigromacs, but the solution given there, to simply erase the second default line does not suit me here. Once I do this, i mean, go to my ligand.itp file and put a ; before my default section, grompp does not recognize anymore that my ligand is there and gives out another error line. I would like some advice on the matter if possible. Thank you in advance Fabrício Bracht >Well, it's not like grompp is recognizing you have a ligand there >right now, is it? grompp doesn't reach the point where it realizes you >don't seem to have a ligand. It seems there's something wrong with the >topology. Better post ligand.itp, like Justin suggests, and also give >the error which occurs when you do comment out the defaults line in >the ligand topology. > >Cheers, > >Tsjerk " Now, the actual itp file. ; M_E.top created by acpypi on Wed Nov 26 18:00:37 2008 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb oo 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 cc 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 oh oh 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 ho ho 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. c3 c3 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 hc hc 0.0 0.0 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157 c2 c2 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ha ha 0.0 0.0 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 ce ce 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 cf cf 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 [ moleculetype ] ;namenrexcl M_E 3 [ atoms ] ; nr type resi res atom cgnr charge mass typeBchargeB 1o 1M_E O491 -0.55230 16.0 ; qtot -0.552 2c 1M_E C482 0.63200 12.01000 ; qtot 0.080 3 oh 1M_E O503 -0.60900 16.0 ; qtot -0.529 4 ho 1M_E H514 0.44690 1.00800 ; qtot -0.082 5 c3 1M_E C455 -0.12590 12.01000 ; qtot -0.208 6 hc 1M_E H466 0.08080 1.00800 ; qtot -0.127 7 hc 1M_E H477 0.08110 1.00800 ; qtot -0.046 8 c3 1M_E C428 -0.07210 12.01000 ; qtot -0.118 9 hc 1M_E H439 0.06640 1.00800 ; qtot -0.052 10 hc 1M_E H44 10 0.05040 1.00800 ; qtot -0.002 11 c3 1M_E C39 11 -0.05170 12.01000 ; qtot -0.053 12 hc 1M_E H40 12 0.04490 1.00800 ; qtot -0.008 13 hc 1M_E H41 13 0.05410 1.00800 ; qtot 0.046 14 c2 1M_E C37 14 -0.16730 12.01000 ; qtot -0.122 15 ha 1M_E H38 15 0.11950 1.00800 ; qtot -0.002 16 c2 1M_E C35 16 -0.16710 12.01000 ; qtot -0.169 17 ha 1M_E H36 17 0.11730 1.00800 ; qtot -0.052 18 c3 1M_E C32 18 -0.04940 12.01000 ; qtot -0.101 19 hc 1M_E H33 19 0.07250 1.00800 ; qtot -0.029 20 hc 1M_E H34 20 0.06180 1.00800 ; qtot 0.033 21 c3 1M_EC2 21 -0.00340 12.01000 ; qtot 0.030 22 hc 1M_EH6 22 0.07250 1.00800 ; qtot 0.102 23 c2 1M_EC1 23 -0.10390 12.01000 ; qtot -0.002 24 ha 1M_EH8 24 0.14850 1.00800 ; qtot 0.147 25 ce 1M_EC5 25 -0.25360 12.01000 ; qtot -0.107 26 ha 1M_EH9 26 0.16130 1.00800 ; qtot 0.054 27c 1M_EC4 27 0.56070 12.01000 ; qtot 0.615 28o 1M_EO7 28 -0.52650 16.0 ; qtot 0.089 29 ce 1M_EC3 29 -0.21970 12
