I had problems having not used gromacs in years a couple years ago. Try running it through with the output as a pdb from pdb2gmx, cut off all headers, and you can then just compare the two files in gedit emacs or word and see differences. That might help. I routinely just keep everything in pdb format as its easier than jumping back and forth.
-------- Original-Nachricht -------- > Datum: Thu, 21 Mar 2013 21:43:16 +0100 > Von: Mark Abraham <mark.j.abra...@gmail.com> > An: Discussion list for GROMACS users <gmx-users@gromacs.org> > Betreff: Re: [gmx-users] help with chromophore of a GFP > On Thu, Mar 21, 2013 at 4:30 PM, Anna MARABOTTI <amarabo...@unisa.it> > wrote: > > > > > > > Dear Mark, > > > > thank you for your message. I'm happy to be on the > > right track; unfortunately the end point seems to be very far away... > > > > > > I tried to obtain that CFY hydrogens and protein hydrogens are all > > matching the aminoacids.rtp entry, in order to avoid dealing with > > aminoacids.hdb. This is what I did: > > > > - starting from the pdb file of > > the protein, I removed CFY entry (prot_noCFY.pdb) > > > > - I used pdb2gmx to > > add H to the protein only: pdb2gmx -f prot_noCFY.pdb -o prot_noCFY_H.pdb > > -p topol.top > > > > - I inserted CFY_H.pdb (obtained with Pymol in a previous > > passage in which I added H with Pymol to the protein, including CFY) > > into prot_noCFY_H.pdb, obtaining prot_CFY_H.pdb. > > > > In this way, H atoms > > bound to "regular" residues have been added using Amber99SB, therefore > > they are compatible with this ff, and atoms of CFY (previously added > > with Pymol) have the same naming convention in aminoacids.rtp (that I > > edited using atom types, charges etc. calculated with Antechamber on > > this molecule coming from Pymol). Obviously, the atom numbering is not > > sequential: the last atom of V63 (the last "regular" residue before CFY) > > is numbered 938, the first atom of H68 (the first "regular" residue > > after CFY) is numbered 939, and the atoms of CFY66 are numbered from 1 > > to 70. Moreover, since the sequence of atoms in aminoacids.rtp is not > > the same as in the coordinates of CFY (I adapted the sequence of atoms > > following the format of other residues in aminoacids.rtp), the numbering > > of CFY in the prot_CFY_H.pdb is not ordered (1-2-3-....-69-70) but > > disordered (19-54-20-55...49-50-24-25). > > > > Seems fine. pdb2gmx is mostly about atom/residue naming. grompp is mostly > about atom/residue/moleculetype ordering. > > - At this stage, I used > > pdb2gmx again to create the topol.top file with all coordinates correct: > > > > > > pdb2gmx -f prot_CFY_H.pdb -o prot_complete.gro -p topol.top > > > > > > (selecting amber99sb forcefield and tip3p for water, as recommended > > option) > > > > This is the message error from pdb2gmx: > > > > Read 'FLUORESCENT > > PROTEIN', 3346 atoms > > Analyzing pdb file > > Splitting PDB chains based on > > TER records or changing chain id. > > There are 1 chains and 0 blocks of > > water and 218 residues with 3346 atoms > > > > chain #res #atoms > > 1 'A' 213 > > 3346 > > > > I'd be concerned about the difference in residue count here, but 4.5.4 is > so old I've no idea whose fault this is. > > > > All occupancies are one > > Opening force field file > > ./amber99sb.ff/atomtypes.atp > > Atomtype 1 > > Reading residue database... > > (amber99sb) > > Opening force field file > > ./amber99sb.ff/aminoacids.rtp > > Residue 94 > > Sorting it all out... > > Opening > > force field file ./amber99sb.ff/dna.rtp > > Residue 110 > > Sorting it all > > out... > > Opening force field file ./amber99sb.ff/rna.rtp > > Residue > > 126 > > Sorting it all out... > > Opening force field file > > ./amber99sb.ff/aminoacids.hdb > > Opening force field file > > ./amber99sb.ff/dna.hdb > > Opening force field file > > ./amber99sb.ff/rna.hdb > > Opening force field file > > ./amber99sb.ff/aminoacids.n.tdb > > Opening force field file > > ./amber99sb.ff/aminoacids.c.tdb > > > > Processing chain 1 'A' (3346 atoms, 213 > > residues) > > There are 327 donors and 319 acceptors > > There are 539 hydrogen > > bonds > > Will use HISE for residue 22 > > Will use HISD for residue 38 > > Will use > > HISE for residue 62 > > Will use HISE for residue 68 > > Will use HISD for > > residue 109 > > Will use HISE for residue 119 > > Will use HISE for residue > > 172 > > Will use HISH for residue 193 > > Will use HISH for residue 197 > > Will use > > HISE for residue 217 > > Identified residue SER3 as a starting > > terminus. > > Identified residue SER218 as a ending terminus. > > 8 out of 8 > > lines of specbond.dat converted successfully > > Special Atom Distance > > matrix: > > MET9 MET11 MET15 HIS22 HIS38 MET41 MET47 > > SD110 SD149 SD232 > > NE2317 NE2549 SD596 SD700 > > MET11 SD149 0.807 > > MET15 SD232 2.279 1.627 > > > > HIS22 NE2317 3.707 2.983 1.466 > > HIS38 NE2549 1.401 0.928 2.127 3.254 > > > > MET41 SD596 1.458 0.665 1.144 2.384 1.001 > > MET47 SD700 3.059 2.324 0.995 > > 0.801 2.656 1.761 > > MET53 SD777 2.786 1.999 0.990 1.171 2.160 1.373 > > 0.603 > > HIS62 NE2917 2.340 1.733 0.833 1.797 1.988 1.236 1.583 > > HIS68 > > NE21002 0.884 0.597 1.466 2.916 1.356 0.885 2.347 > > HIS109 NE21638 2.061 > > 1.886 1.380 2.614 2.661 1.862 2.279 > > HIS119 NE21803 1.459 0.967 0.923 > > 2.372 1.617 0.812 1.870 > > MET135 SD2041 3.480 2.751 1.316 0.606 2.919 > > 2.121 0.993 > > MET162 SD2439 2.521 1.976 1.656 2.412 1.855 1.543 2.264 > > > > HIS172 NE22588 3.632 2.949 1.894 1.657 2.872 2.338 1.945 > > CYS174 SG2623 > > 2.968 2.372 1.452 1.861 2.428 1.848 1.924 > > MET189 SD2891 2.167 2.379 > > 2.736 4.000 2.754 2.569 3.722 > > HIS193 NE22942 2.003 2.001 2.490 3.686 > > 2.049 2.075 3.396 > > HIS197 NE23011 2.012 1.634 1.830 2.896 1.554 1.426 > > 2.614 > > HIS217 NE23329 2.545 2.376 2.831 3.805 2.039 2.305 3.575 > > MET53 > > HIS62 HIS68 HIS109 HIS119 MET135 MET162 > > SD777 NE2917 NE21002 NE21638 > > NE21803 SD2041 SD2439 > > HIS62 NE2917 1.363 > > HIS68 NE21002 2.107 1.482 > > > > HIS109 NE21638 2.365 1.568 1.372 > > HIS119 NE21803 1.688 0.976 0.584 > > 1.078 > > MET135 SD2041 1.057 1.365 2.661 2.490 2.119 > > MET162 SD2439 1.878 > > 0.871 1.805 2.246 1.520 1.861 > > HIS172 NE22588 1.721 1.401 2.829 2.860 > > 2.359 1.067 1.342 > > CYS174 SG2623 1.694 0.725 2.140 2.152 1.681 1.297 > > 0.745 > > MET189 SD2891 3.547 2.310 1.858 1.893 1.980 3.627 2.290 > > HIS193 > > NE22942 3.076 1.890 1.639 2.197 1.760 3.221 1.547 > > HIS197 NE23011 2.229 > > 1.149 1.407 2.078 1.323 2.401 0.676 > > HIS217 NE23329 3.146 2.112 2.205 > > 2.935 2.272 3.263 1.402 > > HIS172 CYS174 MET189 HIS193 HIS197 > > NE22588 > > SG2623 SD2891 NE22942 NE23011 > > CYS174 SG2623 0.826 > > MET189 SD2891 3.417 > > 2.599 > > HIS193 NE22942 2.831 2.079 1.020 > > HIS197 NE23011 2.011 1.324 > > 1.766 0.939 > > HIS217 NE23329 2.629 2.068 1.936 0.946 1.003 > > Opening force > > field file ./amber99sb.ff/aminoacids.arn > > Opening force field file > > ./amber99sb.ff/dna.arn > > Opening force field file > > ./amber99sb.ff/rna.arn > > Checking for duplicate atoms.... > > Now there are > > 3345 atoms. Deleted 1 duplicates. > > > > That also looks suspicious. > > > > Now there are 213 residues with 3345 > > atoms > > Making bonds... > > Warning: Long Bond (988-989 = 0.453624 > > nm) > > > > That seems like it might be a peptide bond bridging a "gap" where pdb2gmx > was unable to recognize the intervening content as a peptide residue. > > > > > > WARNING: atom O1 is missing in residue CFY 66 in the pdb > > file > > > > ------------------------------------------------------- > > Program > > pdb2gmx_d, VERSION 4.5.4 > > Source code file: pdb2top.c, line: 1463 > > > > Fatal > > error: > > There were 1 missing atoms in molecule Protein_chain_A, if you > > want to use this incomplete topology anyhow, use the option -missing > > For > > more information and tips for troubleshooting, please check the > > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > > > The > > strange thing is that I checked for this error, but atom O1 in residue > > CFY66 is present BOTH in the starting .pdb file (the one I used for > > pdb2gmx) AND in the aminoacids.rtp file!!!! I checked 4 or 5 times, > > every time erasing the old file, checking the file IMMEDIATELY BEFORE > > submitting it to pdb2gmx. All atoms present in aminoacids.rtp for CFY > > residue are also present in the .pdb file and vice versa, and I am sure > > I did not make the stupid error of naming the atom 01 (zero-one) instead > > of O1 (o-one). > > > > I suspect that this atom is the one which is deleted > > because recognized as duplicated, but I'm not sure about it and I don't > > know how to check it. I am sure there are no duplicated atoms in CFY. > > > > > > I feel like this is a "fake" error message (i.e.: there is an error in > > my files, but it is not the one that is reported in the message: > > probably a problem occur around this atom, but it is not exactly ON this > > atom). However, I am not able to find errors. > > > > Hmm that seems weird. Justin's theory sounds plausible, but I haven't seen > someone stumble on that before. Also plausible is that pdb2gmx thinks your > CFY is a disconnected part of the chain and needs terminating (which might > happen with an oxygen named O1?). > > It's possible there's buggy behaviour here that has been fixed in the two > years since that code was released. There certainly has been an upgrade of > the "is this really a new chain" machinery. Unless you have a strong > scientific reason to keep 4.5.4, I'd switch to 4.6.1 (or 4.5.6 if you > really have to keep 4.5). If Justin's fix doesn't work, and you have > problems with a more recent version, then we can look closer. > > > > BTW the "long bond" of > > the other warning message is not involving residue CFY. > > > > Yeah, but my bet is those atoms are the C-terminus and N-terminus of the > fragments that should form peptide bonds to CFY. > > Mark > > > > Any help is > > welcome > > > > Thank you so much. > > > > Anna > > > > Il 21.03.2013 12:00 > > gmx-users-requ...@gromacs.org ha scritto: > > > > >> Dear gmx-users, it's > > about two weeks that I'm trying to solve this problem, and I can't, so > > I'm asking your help. I want to do some MD simulations on a protein of > > the family of green fluorescent protein. This protein, as you know, has > > a chromophore (CFY) derived from four residues of the protein > > (F64-C65-Y66-G67) and covalently bound to the rest of the protein chain. > > How to parametrize this object, since it is not recognized by pdb2gmx? I > > looked at the gmx-users list and the suggestion was to create a new > > entry in the .rtp file of the selected forcefield. > > > > > > Indeed, this > > kind of problem is most easily solved by making a new > > > "residue" that > > contains the whole chromophore, such that it links to its > > > neighbours > > with normal peptide links. > > > ------------------------------ Message: 5 > > Date: Thu, 21 Mar 2013 11:46:12 +0100 From: Mark Abraham > > <mark.j.abra...@gmail.com [2]> Subject: Re: [gmx-users] help with > > chromophore of a GFP To: Discussion list for GROMACS users > > <gmx-users@gromacs.org [3]> Message-ID: > > <camnumasicymgivb_x5sy1yb44th8vknioqvhzdqq-tam9tn...@mail.gmail.com [4]> > > Content-Type: text/plain; charset=ISO-8859-1 On Wed, Mar 20, 2013 at > > 6:01 PM, Anna MARABOTTI <amarabo...@unisa.it [5]> wrote: > > > > > >> I > > decided to use Amber99SB since it seemed the better for my scope, then I > > start trying to parameterize it. This is what I did: * I used Pymol to > > add H to my pdb file, since I want to use an all H forcefield and since > > Antechamber (see below) does not work without H * I extracted the > > segment V63-CFY-H68 from my .pdb file. I did this since, when I > > extracted CFY only, I had problems with the terminals * Following the > > Antechamber tutorial, I used Antechamber (using the traditional Amber > > force field, not GAFF) to calculate charges and to assign atom types to > > this segment. * I used these calculated parameters in order to add the > > CFY residue to aminoacids.rtp in amber99sb.ff directory. * I tried to > > modify also aminoacids.hdb, but since it seemed too complicated to me, I > > decided to keep it unchanged, and to give pdb2gmx the protein with H > > already present * No need to add new atom/bond types to ffbonded.itp and > > ffnonbonded.itp: they seem all present. Since CFY is bound to the rest > > of protein with common peptide bonds, I did not change specbond.dat > > either. * I added CFY in residuetypes.dat with the specification > > "Protein" In my opinion, all was ready to go, instead... When I launched > > pdb2gmx to my protein with H added by PyMol, I got immediately an error: > > Fatal error: Atom H01 in residue SER 3 was not found in rtp entry NSER > > with 13 atoms while sorting atoms. For a hydrogen, this can be a > > different protonation state, or it might have had a different number in > > the PDB file and was rebuilt (it might for instance have been H3, and we > > only expected H1 & H2). Note that hydrogens might have been added to the > > entry for the N-terminus. Remove this hydrogen or choose a different > > protonation state to solve it. Option -ignh will ignore all hydrogens in > > the input. For more information and tips for troubleshooting, please > > check the GROMACS website at http://www.gromacs.org/Documentation/Errors > > [1][1] > > >> > > >>> From this error I > > >> understand that: * the code for H > > in PyMol is different from the code for H in Amber (read from > > aminoacids.rtp); in order to correct this error, I should add -ignh in > > order to ignore H in input. > > > > > > pdb2gmx has to be able to make sense of > > the atom naming. There are lots of > > > different conventions for how to > > name atoms, particularly hydrogen atoms. > > > pdb2gmx can't possibly encode > > the logic to convert all of those > > > conventions. So the path of least > > resistance can be to ignore hydrogens and > > > regenerate them according to > > the generation rules. > > > > > > However, you can just rename them in the > > input file so that pdb2gmx > > > understands your meaning. The NSER entry in > > the .rtp file shows you the > > > names pdb2gmx expects. If you edit the > > names of those hydrogen atoms > > > (probably H01, H02, H03) in your input > > coordinate file accordingly (to H1, > > > H2, H3), things will be fine. Be > > sure you don't break the required column > > > formatting of the coordinate > > file! > > > > > > * > > > > > > > > Links: > > ------ > > [1] > > http://www.gromacs.org/Documentation/Errors > > [2] > > mailto:mark.j.abra...@gmail.com > > [3] mailto:gmx-users@gromacs.org > > [4] > > > mailto:camnumasicymgivb_x5sy1yb44th8vknioqvhzdqq-tam9tn...@mail.gmail.com > > [5] > > mailto:amarabo...@unisa.it > > -- > > 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 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 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
