[gmx-users] Capping (neuralising) of peptide
David van der Spoel
spoel at xray.bmc.uu.se
Thu Sep 30 14:16:04 CEST 2004
On Thu, 2004-09-30 at 14:04, Alok wrote:
> Hello
> As i generated the pdb file of tripeptide (GPG) using insight. After
> capping (neuralising) of that peptide on both N and C terminal (i changed
> glycines N terminal to NH2 and second glycines C terminal to COOH).
> But now i am geeting another problem as these GLY residues are not define
> in .rtp file.so following error comes up after pdb2gmx.
>
pdb2gmx -ter -ignh
>
>
>
> Select the Force Field:
> 0: GROMOS96 43a1 Forcefield (official distribution)
> 1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
> 2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals) 3:
> OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> 4: Gromacs Forcefield (see manual)
> 5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)
> 0
> Looking whether force field file ffG43a1.rtp exists
> Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
> Opening library file /usr/local/share/gromacs/top/aminoacids.dat
> Reading peptide.pdb...
> Read 124 atoms
> Opening library file /usr/local/share/gromacs/top/xlateat.dat
> 23 out of 23 lines of xlateat.dat converted succesfully
> Analyzing pdb file
> There are 1 chains and 0 blocks of water and 16 residues with 124 atoms
>
> chain #res #atoms
> 1 ' ' 16 124
>
> WARNING: there were 0 atoms with zero occupancy and 1 atoms with
> occupancy unequal to one (out of 124 atoms). Check your pdb file.
> Opening library file /usr/local/share/gromacs/top/ffG43a1.atp
> Atomtype 50
> Reading residue database... (ffG43a1)
> Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
> Residue 96
> Sorting it all out...
> Opening library file /usr/local/share/gromacs/top/ffG43a1.hdb
> Opening library file /usr/local/share/gromacs/top/ffG43a1-n.tdb
> Opening library file /usr/local/share/gromacs/top/ffG43a1-c.tdb
>
> Back Off! I just backed up peptide.top to ./#peptide.top.7#
> Processing chain 1 (124 atoms, 16 residues)
> Opening library file /usr/local/share/gromacs/top/specbond.dat
> 5 out of 5 lines of specbond.dat converted succesfully
> There are 12 donors and 16 acceptors
> There are 19 hydrogen bonds
> Fatal error: Atom HA1 in residue GLY 1 not found in rtp entry with 5 atoms
> while sorting atoms. Maybe different protonation state.
> Remove this hydrogen or choose a different protonation state.
> Option -ignh will ignore all hydrogens in the input.
>
>
>
>
> so now what I have to do now? should i define these GLY residue in .rtp
> file?? Or anything else??
>
> i am attaching pdb file also.
>
>
>
>
> ATOM 1 N GLY 1 15.055 26.899 27.745 1.00 0.00
> N
> ATOM 2 CA GLY 1 14.262 27.999 27.204 1.00 0.00
> C
> ATOM 3 C GLY 1 14.753 29.328 27.725 1.00 0.00
> C
> ATOM 4 O GLY 1 15.669 29.411 28.537 1.00 0.00
> O
> ATOM 5 1H GLY 1 15.783 27.276 28.371 1.00 0.00
> H
> ATOM 6 2H GLY 1 14.444 26.262 28.276 1.00 0.00
> H
> ATOM 7 1HA GLY 1 14.313 28.000 26.100 1.00 0.00
> H
> ATOM 8 2HA GLY 1 13.198 27.873 27.476 1.00 0.00
> H
> ATOM 9 N PRO 1B 14.138 30.394 27.257 1.00 0.00
> N
> ATOM 10 CA PRO 1B 14.502 31.745 27.655 1.00 0.00
> C
> ATOM 11 C PRO 1B 14.016 32.068 29.078 1.00 0.00
> C
> ATOM 12 O PRO 1B 12.967 31.584 29.504 1.00 0.00
> O
> ATOM 13 CB PRO 1B 13.737 32.594 26.628 1.00 0.00
> C
> ATOM 14 CG PRO 1B 12.506 31.737 26.294 1.00 0.00
> C
> ATOM 15 CD PRO 1B 13.059 30.311 26.295 1.00 0.00
> C
> ATOM 16 HA PRO 1B 15.585 31.876 27.616 1.00 0.00
> H
> ATOM 17 1HB PRO 1B 13.474 33.584 27.007 1.00 0.00
> H
> ATOM 18 2HB PRO 1B 14.352 32.706 25.731 1.00 0.00
> H
> ATOM 19 1HG PRO 1B 11.763 31.839 27.088 1.00 0.00
> H
> ATOM 20 2HG PRO 1B 12.057 32.005 25.335 1.00 0.00
> H
> ATOM 21 1HD PRO 1B 12.312 29.578 26.607 1.00 0.00
> H
> ATOM 22 2HD PRO 1B 13.464 30.046 25.315 1.00 0.00
> H
> ATOM 23 N GLY 1C 14.726 32.860 29.852 1.00 0.00
> N
> ATOM 24 CA GLY 1C 14.238 33.314 31.151 1.00 0.00
> C
> ATOM 25 C GLY 1C 13.769 34.748 31.082 1.00 0.00
> C
> ATOM 26 O GLY 1C 13.445 35.378 32.087 1.00 0.00
> O
> ATOM 27 H GLY 1C 15.654 33.172 29.532 1.00 0.00
> H
> ATOM 28 1HA GLY 1C 13.403 32.675 31.489 1.00 0.00
> H
> ATOM 29 2HA GLY 1C 15.036 33.230 31.910 1.00 0.00
> H
> ATOM 30 O OH 2 13.704 35.373 29.853 1.00 0.00
> O
> ATOM 31 HO OH 2 13.391 36.273 29.966 1.00 0.00
> H
>
>
>
> Thanks!
>
> Alok
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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