[gmx-users] trouble with ca2+ atom and SEP recognition in Gromacs 5.1.1
Jayant James
jayant.james at gmail.com
Wed Apr 20 21:56:11 CEST 2016
Hi!
All I have been running into some trouble with CA2+ recognition in GMX
5.1.1.
So some back ground......I have a protein that I am trying to simulate that
has three chains.First chain is 161 amino acids long, second one is about
200AA and the third one is about 280 AA long.
They have their terminal residues given with OXT and "ter" is given after
each chain. Also this protein has two phosphorylated serines that are input
as SEP.
Since I am having two SEP molecules I am using the option#
10 GROMOS96 43a1 force field, extended to include phosphorylated residues
Below is the description of the calcium atoms in the input PDB file
-------------------------------------------------------------------------------------------
ATOM 1283 CA CA2+D 162 10.494 65.413 -1.733 1.00
78.08 C
ATOM 1284 CA CA2+D 163 14.370 25.685 8.168 1.00
78.08 C
ATOM 1285 CA CA2+D 164 18.826 35.294 3.395 1.00
78.08 C
INPUT COMMAND
--------------------------
gmx pdb2gmx -f start.pdb -p new -o new -merge all -ignh
Concerns
-------------
1) I am hit with error messages that tell me the calcium ions are not
recognized (colored red). I'd appreciate a way to solve this.
2) Also the third chain having the SEP amino acids is not being
recognizing!!! Colored blue
3) The third chain is 192 aa long. But the program tells that it recognizes
only till 22 aa although a few lines this it seems like it recognizes till
the 192nd aa
I'd appreciate any suggetions that would help me tide over these errors
Thank you
James
*ERROR MESSAGE*
--------------------------
Opening force field file
/share/apps/gromacs/5.1.1/share/gromacs/top/gromos43a1p.ff/aminoacids.r2b
Reading start.pdb...
Read 3572 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
Merged chains into joint molecule definitions at 2 places.
There are 1 chains and 0 blocks of water and 443 residues with 3572 atoms
chain #res #atoms
1 'D' 443 3572
All occupancies are one
Opening force field file
/share/apps/gromacs/5.1.1/share/gromacs/top/gromos43a1p.ff/atomtypes.atp
Atomtype 48
Reading residue database... (gromos43a1p)
Opening force field file
/share/apps/gromacs/5.1.1/share/gromacs/top/gromos43a1p.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a proper
dihedral
Residue 101
Sorting it all out...
Opening force field file
/share/apps/gromacs/5.1.1/share/gromacs/top/gromos43a1p.ff/aminoacids.hdb
Opening force field file
/share/apps/gromacs/5.1.1/share/gromacs/top/gromos43a1p.ff/aminoacids.n.tdb
Opening force field file
/share/apps/gromacs/5.1.1/share/gromacs/top/gromos43a1p.ff/aminoacids.c.tdb
Back Off! I just backed up new.top to ./#new.top.2#
Processing chain 1 'D' (3572 atoms, 443 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 679 donors and 705 acceptors were found.
There are 937 hydrogen bonds
Will use HISE for residue 223
Will use HISE for residue 35
Will use HISE for residue 102
Will use HISE for residue 173
Identified residue MET1 as a starting terminus.
Warning: Residue CA2+162 in chain has different type (Other) from starting
residue MET1 (Protein).
Warning: Residue CA2+163 in chain has different type (Other) from starting
residue MET1 (Protein).
Warning: Residue CA2+164 in chain has different type (Other) from starting
residue MET1 (Protein).
Identified residue GLU161 as a ending terminus.
Identified residue GLN202 as a starting terminus.
Identified residue LYS288 as a ending terminus.
Identified residue MET1 as a starting terminus.
Warning: Residue SEP23 in chain has different type (Other) from starting
residue MET1 (Protein).
Warning: Residue SEP24 in chain has different type (Other) from starting
residue MET1 (Protein).
Warning: Residue ALA25 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue ASN26 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue TYR27 in chain has different type (Protein) from starting
residue MET1 (Protein).
Special Atom Distance matrix:
MET1 MET45 MET47 MET60 MET80 MET81 MET85
SD7 SD349 SD368 SD470 SD625 SD633 SD665
MET45 SD349 2.333
MET47 SD368 3.175 1.004
MET60 SD470 1.883 0.496 1.457
MET80 SD625 1.769 0.820 1.424 0.683
MET81 SD633 2.065 0.981 1.341 1.050 0.535
MET85 SD665 2.101 1.580 1.957 1.599 1.186 0.763
MET103 SD811 2.816 4.357 5.164 4.054 3.983 3.945 3.408
MET120 SD951 2.555 4.222 4.965 3.920 3.727 3.671 3.123
MET137 SD1082 1.849 4.018 4.779 3.627 3.383 3.485 3.172
MET157 SD1251 1.551 3.179 3.960 2.854 2.681 2.680 2.231
HIS223 NE21473 7.176 7.929 8.742 7.731 8.007 7.975 7.509
MET1 SD2041 3.767 2.480 1.797 2.734 2.252 2.074 2.527
HIS35 NE22305 1.047 3.366 4.179 2.909 2.763 3.045 3.012
HIS102 NE22835 6.395 7.370 8.229 7.126 7.375 7.374 6.916
MET155 SD3270 2.314 0.740 0.973 0.958 0.595 0.374 1.079
MET156 SD3278 2.603 1.313 1.260 1.541 1.089 0.585 0.840
HIS173 NE23408 5.480 3.326 2.516 3.818 3.786 3.462 3.668
MET103 MET120 MET137 MET157 HIS223 MET1 HIS35
SD811 SD951 SD1082 SD1251 NE21473 SD2041 NE22305
MET120 SD951 0.765
MET137 SD1082 1.912 1.391
MET157 SD1251 1.395 1.078 1.275
HIS223 NE21473 5.003 5.749 6.762 6.162
MET1 SD2041 5.815 5.393 5.030 4.501 9.999
HIS35 NE22305 2.748 2.420 1.262 1.747 7.244 4.560
HIS102 NE22835 4.192 4.937 5.879 5.383 1.003 9.418 6.376
MET155 SD3270 4.265 4.019 3.824 3.016 8.157 1.940 3.313
MET156 SD3278 4.242 3.948 3.877 3.031 8.215 1.790 3.553
HIS173 NE23408 6.790 6.650 6.836 5.825 9.678 3.077 6.495
HIS102 MET155 MET156
NE22835 SD3270 SD3278
MET155 SD3270 7.579
MET156 SD3278 7.656 0.624
HIS173 NE23408 9.382 3.206 3.020
Start terminus MET-1: NH3+
End terminus GLU-161: COO-
Start terminus GLN-202: NH3+
End terminus LYS-288: COO-
Start terminus MET-1: NH3+
End terminus ARG-22: COO-
-------------------------------------------------------
Program gmx pdb2gmx, VERSION 5.1.1
Source code file:
/share/apps/gromacs/5.1.1/build/gromacs-5.1.1/src/gromacs/gmxpreprocess/pdb2gmx.c,
line: 746
Fatal error:
Atom OXT in residue TRP 192 was not found in rtp entry TRP with 21 atoms
while sorting atoms.
.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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