Hi Mark Thanks for the rtp definitions. I added the rtp defs to aminoacids.rtp and renamed residue and atom names in pdb file.
But pdb2gmx is still complaining about the terminal groups. It seems to have picked up ACE, but not CT3. pdb2gmx error message and modified pdb file are listed below. Any idea ? Do I need to modify .c.tdb ? If so, do you have that entry as well :) ? Thanks Sandeep =============pdb2gmx error======================================= Back Off! I just backed up topol.top to ./#topol.top.3# Processing chain 1 (32 atoms, 4 residues) There are 3 donors and 3 acceptors There are 4 hydrogen bonds Identified residue ACE1 as a starting terminus. Warning: Residue CT32 in chain has different type (Other) from starting residue ACE1 (Protein). Identified residue ALA2 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Start terminus ACE-1: NH3+ End terminus ALA-2: COO- ------------------------------------------------------- Program pdb2gmx_d, VERSION 4.5.4 Source code file: pdb2top.c, line: 1070 Fatal error: atom N not found in buiding block 1ACE while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- ================pdb2gmx error==================================== ================modified pdb===================================== REMARK NONE * REMARK DATE: 8/10/11 5:30:23 CREATED BY USER: ss2029 *ATOM 1 CT3 ACE 1 -2.160 0.537 0.930 1.00 0.00 DIAL* *ATOM 2 HT1 ACE 1 -2.466 0.003 0.005 1.00 0.00 DIAL* *ATOM 3 HT2 ACE 1 -2.562 1.572 0.910 1.00 0.00 DIAL* *ATOM 4 HT3 ACE 1 -2.562 0.001 1.816 1.00 0.00 DIAL* *ATOM 5 C ACE 1 -0.672 0.582 1.009 1.00 0.00 DIAL* *ATOM 6 O ACE 1 -0.105 1.128 1.954 1.00 0.00 DIAL* ATOM 7 N ALA 1 0.000 0.000 0.000 1.00 0.00 DIAL ATOM 8 HN ALA 1 -0.453 -0.444 -0.769 1.00 0.00 DIAL ATOM 9 CA ALA 1 1.459 0.000 0.000 1.00 0.00 DIAL ATOM 10 HA ALA 1 1.812 -0.497 0.897 1.00 0.00 DIAL ATOM 11 CB ALA 1 1.949 -0.834 -1.207 1.00 0.00 DIAL ATOM 12 HB1 ALA 1 1.514 -1.854 -1.155 1.00 0.00 DIAL ATOM 13 HB2 ALA 1 1.628 -0.373 -2.167 1.00 0.00 DIAL ATOM 14 HB3 ALA 1 3.056 -0.932 -1.214 1.00 0.00 DIAL ATOM 15 C ALA 1 2.096 1.401 0.000 1.00 0.00 DIAL ATOM 16 O ALA 1 1.425 2.432 0.000 1.00 0.00 DIAL ATOM 17 N ALA 2 3.451 1.458 0.000 1.00 0.00 DIAL ATOM 18 HN ALA 2 3.954 0.594 0.000 1.00 0.00 DIAL ATOM 19 CA ALA 2 4.276 2.664 0.000 1.00 0.00 DIAL ATOM 20 HA ALA 2 4.065 3.236 -0.897 1.00 0.00 DIAL ATOM 21 CB ALA 2 3.864 3.539 1.207 1.00 0.00 DIAL ATOM 22 HB1 ALA 2 2.776 3.756 1.155 1.00 0.00 DIAL ATOM 23 HB2 ALA 2 4.063 3.014 2.167 1.00 0.00 DIAL ATOM 24 HB3 ALA 2 4.407 4.508 1.214 1.00 0.00 DIAL ATOM 25 C ALA 2 5.791 2.399 0.000 1.00 0.00 DIAL ATOM 26 O ALA 2 6.597 3.328 0.000 1.00 0.00 DIAL *ATOM 27 N CT3 2 6.175 1.110 0.000 1.00 0.00 DIAL* *ATOM 28 HN CT3 2 5.528 0.351 0.000 1.00 0.00 DIAL* *ATOM 29 CT CT3 2 7.566 0.777 0.000 1.00 0.00 DIAL* *ATOM 30 HT1 CT3 2 8.048 1.201 0.907 1.00 0.00 DIAL* *ATOM 31 HT2 CT3 2 7.683 -0.327 0.000 1.00 0.00 DIAL* *ATOM 32 HT3 CT3 2 8.048 1.201 -0.907 1.00 0.00 DIAL* TER 33 CT3 2 END ================modified pdb===================================== On Fri, Sep 9, 2011 at 2:52 AM, Mark Abraham <[email protected]>wrote: > On 9/09/2011 8:05 AM, Sandeep Somani wrote: > >> Hi >> >> I am trying to set up a simulation for dialanine using charmm27 ff but am >> getting errors in pdb2gmx due to missing definitions in rtp file. >> >> I created the pdb file (below) using Charmm for the sequence >> ACE-ALA-ALA-CT3. >> >> pdb2gmx recognizes ALA atoms but not those of the terminal groups ACE and >> CT3. >> > > Yes, CHARMM in GROMACS has lacked these for some time. I asked over a year > ago for them to be added, but that hasn't happened. You can add > > [ ACE ] > [ atoms ] > CT3 CT3 -0.270 0 > HT1 HA 0.090 1 > HT2 HA 0.090 2 > HT3 HA 0.090 3 > C C 0.510 4 > O O -0.510 5 > [ bonds ] > C CT3 > C +N > CT3 HT31 > CT3 HT32 > CT3 HT33 > O C > [ impropers ] > C CT3 +N O > > [ CT3 ] > ; this can also be done with the .c.tdb, but the atom naming is different > ; and this can matter > [ atoms ] > N NH1 -0.470 0 > HN H 0.310 1 > CT CT3 -0.110 2 > HT1 HA 0.090 3 > HT2 HA 0.090 4 > HT3 HA 0.090 5 > [ bonds ] > -C N > N HN > N CAT > CT HT1 > CT HT2 > CT HT3 > > [ impropers ] > N -C CAT HN > -C CAT N -O > > to the end of aminoacids.rtp in a local copy of the charmm27.ff folder to > make this work. > > > >> Does someone have the appropriate definitions for these residues ? >> ( I have tried http://swissparam.ch/ to generate an itp file for the >> molecule, but upon using it in GMX it does not give the same energy as that >> from charmm. ) >> > > That will likely be a separate issue. > > Mark > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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 [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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