[gmx-users] trouble with ca2+ atom and SEP recognition in Gromacs 5.1.1
Justin Lemkul
jalemkul at vt.edu
Thu Apr 21 11:54:23 CEST 2016
On 4/20/16 3:56 PM, Jayant James wrote:
> 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.
They're recognized just fine, but apparently they're disrupting a protein chain.
A continuous chain has to be continuous with respect to residue type,
otherwise pdb2gmx warns you that something is amiss.
> 2) Also the third chain having the SEP amino acids is not being
> recognizing!!! Colored blue
You need to add SEP as a Protein entry in residuetypes.dat.
> 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
See point #2.
-Justin
> 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
> -------------------------------------------------------
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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