[gmx-users] topology for small peptide using amber03
kolnkempff
kolnkempff at gmail.com
Thu Nov 28 04:21:19 CET 2013
/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
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