[gmx-users] topology for small peptide using amber03
Mark Abraham
mark.j.abraham at gmail.com
Thu Nov 28 10:21:48 CET 2013
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Mark
On Nov 28, 2013 4:26 AM, "kolnkempff" <kolnkempff at gmail.com> wrote:
> /I am trying to use pdb2gmx to get a topology for a very simple peptide
> that
> has just three components: an ACE residue followed by phenylananine
> followed by NME
> I've read through the Duan article and it seems that amber03 should be
> ideal
> for this. The pdb file I'm using came from a quantum simulation using
> gamess. I went in by hand to label each atom as belonging to ACE, PHE, or
> NME.
>
> Try #1 All atoms listed as "HETATM"/
>
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.r2b
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/amber03.ff/dna.r2b
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/amber03.ff/rna.r2b
> Reading apn1.pdb...
> WARNING: all CONECT records are ignored
> Read 'UNNAMED', 32 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> There are 1 chains and 0 blocks of water and 1 residues with 32 atoms
>
> chain #res #atoms
> 1 ' ' 3 32
>
> All occupancies are one
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/amber03.ff/atomtypes.atp
> Atomtype 1
> Reading residue database... (amber03)
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.rtp
> Residue 93
> Sorting it all out...
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/amber03.ff/dna.rtp
> Residue 109
> Sorting it all out...
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/amber03.ff/rna.rtp
> Residue 125
> Sorting it all out...
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.hdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/amber03.ff/dna.hdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/amber03.ff/rna.hdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.n.tdb
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.c.tdb
> Processing chain 1 (32 atoms, 3 residues)
> Identified residue PHE1 as a starting terminus.
> Identified residue NME1 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.arn
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/amber03.ff/dna.arn
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/amber03.ff/rna.arn
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.6.4
> Source code file: /home/koln/bin/gromacs-4.6.4/src/kernel/pdb2gmx.c, line:
> 727
>
> Fatal error:
> Atom H in residue ACE 1 was not found in rtp entry ACE with 6 atoms
> while sorting atoms.
>
> /I looked at aminoacids.rtp which lists [ACE] as having 6 atoms. I went
> ahead and checked [PHE] and [NME] and I have the same number and type of
> atoms as they do.
>
> Try #2. After looking at a pdb file for a small neuropeptide I decided to
> try labeling everything as "ATOM" rather than 'HETATM"
> [first part is same as before]/
>
> Warning: Starting residue E1 in chain not identified as Protein/RNA/DNA.
> Problem with chain definition, or missing terminal residues.
> This chain does not appear to contain a recognized chain molecule.
> If this is incorrect, you can edit residuetypes.dat to modify the behavior.
> 8 out of 8 lines of specbond.dat converted successfully
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.6.4
> Source code file: /home/koln/bin/gromacs-4.6.4/src/kernel/resall.c, line:
> 642
>
> Fatal error:
> Residue 'E' not found in residue topology database
>
> /Try #3. I labeled the phenylalanine atoms as "ATOM" and the terminal ACE
> and NME atoms as "HETATM"/
> Warning: Starting residue E1 in chain not identified as Protein/RNA/DNA.
> Identified residue ACE1 as a starting terminus.
> Identified residue NME1 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.6.4
> Source code file: /home/koln/bin/gromacs-4.6.4/src/kernel/resall.c, line:
> 642
>
> Fatal error:
> Residue 'E' not found in residue topology database
>
> /I have no idea where "Residue 'E'" came from.
> Since the third try seems to be closest to "working", that's the one I am
> including below.
>
> Thanks in advance for whatever help you can offer.
>
> Koln/
>
> pdb file:COMPND UNNAMED
> AUTHOR GENERATED BY OPEN BABEL 2.3.1
> ATOM 1 N PHE 1 0.720 0.859 -0.499 1.00 0.00
> N
> ATOM 2 C PHE 1 0.760 -0.439 0.174 1.00 0.00
> C
> ATOM 3 C PHE 1 2.125 -1.161 0.111 1.00 0.00
> C
> ATOM 4 O PHE 1 2.253 -2.263 0.634 1.00 0.00
> O
> ATOM 5 H PHE 1 0.176 0.905 -1.352 1.00 0.00
> H
> ATOM 6 H PHE 1 0.585 -0.253 1.240 1.00 0.00
> H
> ATOM 7 C PHE 1 -0.336 -1.383 -0.373 1.00 0.00
> C
> ATOM 8 C PHE 1 -1.743 -0.858 -0.186 1.00 0.00
> C
> ATOM 9 H PHE 1 -0.200 -2.340 0.138 1.00 0.00
> H
> ATOM 10 H PHE 1 -0.145 -1.567 -1.440 1.00 0.00
> H
> ATOM 11 C PHE 1 -4.354 0.139 0.179 1.00 0.00
> C
> ATOM 12 C PHE 1 -2.316 -0.794 1.094 1.00 0.00
> C
> ATOM 13 C PHE 1 -2.504 -0.416 -1.277 1.00 0.00
> C
> ATOM 14 C PHE 1 -3.799 0.078 -1.100 1.00 0.00
> C
> ATOM 15 C PHE 1 -3.607 -0.301 1.276 1.00 0.00
> C
> ATOM 16 H PHE 1 -1.744 -1.138 1.954 1.00 0.00
> H
> ATOM 17 H PHE 1 -2.086 -0.476 -2.281 1.00 0.00
> H
> ATOM 18 H PHE 1 -4.373 0.412 -1.961 1.00 0.00
> H
> ATOM 19 H PHE 1 -4.033 -0.263 2.276 1.00 0.00
> H
> ATOM 20 H PHE 1 -5.362 0.519 0.320 1.00 0.00
> H
> HETATM 21 C ACE 1 0.873 2.036 0.208 1.00 0.00
> C
> HETATM 22 O ACE 1 1.301 2.055 1.353 1.00 0.00
> O
> HETATM 23 C ACE 1 0.484 3.302 -0.540 1.00 0.00
> C
> HETATM 24 H ACE 1 1.253 4.060 -0.375 1.00 0.00
> H
> HETATM 25 H ACE 1 -0.451 3.685 -0.116 1.00 0.00
> H
> HETATM 26 H ACE 1 0.345 3.153 -1.616 1.00 0.00
> H
> HETATM 27 N NME 1 3.115 -0.507 -0.549 1.00 0.00
> N
> HETATM 28 C NME 1 4.474 -1.010 -0.616 1.00 0.00
> C
> HETATM 29 H NME 1 5.163 -0.381 -0.040 1.00 0.00
> H
> HETATM 30 H NME 1 4.474 -2.015 -0.195 1.00 0.00
> H
> HETATM 31 H NME 1 4.822 -1.054 -1.654 1.00 0.00
> H
> HETATM 32 H NME 1 2.906 0.422 -0.885 1.00 0.00
> H
> CONECT 1 5 2 21
> CONECT 2 1 7 3 6
> CONECT 2
> CONECT 3 27 2 4
> CONECT 4 3
> CONECT 5 1
> CONECT 6 2
> CONECT 7 10 8 9 2
> CONECT 7
> CONECT 8 13 7 12
> CONECT 9 7
> CONECT 10 7
> CONECT 11 14 20 15
> CONECT 12 8 15 16
> CONECT 13 17 14 8
> CONECT 14 18 13 11
> CONECT 15 11 12 19
> CONECT 16 12
> CONECT 17 13
> CONECT 18 14
> CONECT 19 15
> CONECT 20 11
> CONECT 21 23 1 22
> CONECT 22 21
> CONECT 23 26 24 25 21
> CONECT 23
> CONECT 24 23
> CONECT 25 23
> CONECT 26 23
> CONECT 27 32 28 3
> CONECT 28 31 27 30 29
> CONECT 28
> CONECT 29 28
> CONECT 30 28
> CONECT 31 28
> CONECT 32 27
> MASTER 0 0 0 0 0 0 0 0 32 0 32 0
> END
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/topology-for-small-peptide-using-amber03-tp5012868.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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