<html><head></head><body style="visibility: visible;">Dear All
<br />
I searched my problem in users mailing list but I could not find the
answer. please help me with this.<br />I am learning the CG Martini force
filed using the tutorial
"protein in water" for protein ubiquitin. so I did the things like
below:
<br />
<br />1. awk -f atom2cg_v2.1.awk 1UBQ.pdb > 1UBQ-cg.pdb (it makes a CG
.pdb file)
<br />
<br />2. wget ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt
<br />
<br />3. grep -A 1 1ubq pdb_seqres.txt > 1ubq.seq (these 2 and 3
commands make a .seq file)
<br />
<br />4. ./seq2itp.pl 1ubq.seq 1ubq.ssd > 1ubq.itp (by the use of .seq
and .ssd file and seq2itp.pl script I can make a .itp file. I should
mention that I used .ssd file prepared by matini group in this
tutorial.)
<br />
<br />5. I make a 1ubq.top file like below
<br />
<br />#include "martini_v2.1.itp"
<br />#include "1ubq.itp"
<br />
<br />[ system ]
<br />; name
<br />protein
<br />
<br />[ molecules ]
<br />; name number
<br />protein 1
<br />
<br />6. grompp -f 1ubq.mdp -c 1UBQ-cg.pdb -p 1ubq.top
<br />
<br />but warnings come like this
<br />
<br />Warning: atom name 1 in 1ubq.top and 1UBQ-cg.pdb does not match (BBc
- BB)
<br />Warning: atom name 2 in 1ubq.top and 1UBQ-cg.pdb does not match (S1c
- S1)
<br />Warning: atom name 3 in 1ubq.top and 1UBQ-cg.pdb does not match (BBe
- BB)
<br />............
<br />
<br />............
<br />
<br />all of my atom names mismatch. I checked the 1ubq.itp. some lines
are in below
<br />
<br />;;; MARTINI 2.1 coarse-grained topology
<br />;;; Generated by seq2itp.pl version 1.1.4
<br />
<br />;;; SEQ: MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL 50
<br />;;; SEQ: EDGRTLSDYN IQKESTLHLV LRLRGG
<br />;;; Total Number of Amino Acid Residues: 76
<br />
<br />
<br />[moleculetype]
<br />;molname exclusions
<br />Protein 1
<br />
<br />[atoms]
<br />1 Qd 1 MET BBc 1 1.000 ; COI
<br />2 C5 1 MET S1c 2 0.000 ; COI
<br />3 Nda 2 GLN BBe 3 0.000 ; EXT
<br />
<br />........
<br />
<br />........
<br />
<br />[ bonds ]
<br />;backbone-backbone bonds
<br />1 3 1 0.350 400 ; COI-EXT
<br />3 5 1 0.350 1250 ; EXT-EXT
<br />5 7 1 0.350 1250 ; EXT-EXT
<br />
<br />........
<br />
<br />........
<br />
<br />[ constraints ]
<br />;sc-sc constraints (Ring Structures)
<br />8 9 1 0.270 ; PHE4
<br />8 10 1 0.270 ; PHE4
<br />9 10 1 0.270 ; PHE4
<br />
<br />.........
<br />
<br />.........
<br />
<br />[angles]
<br />;backbone-backbone-backbone angles
<br />1 3 5 2 127.00 25 ; COI-EXT-EXT
<br />3 5 7 2 134.00 25 ; EXT-EXT-EXT
<br />5 7 11 2 134.00 25 ; EXT-EXT-EXT
<br />
<br />.............
<br />
<br />.............
<br />
<br />[dihedrals]
<br />;improper dihedral angles
<br />7 9 10 8 2 0.00 50 ; PHE4
<br />94 96 97 95 2 0.00 50 ; PHE45
<br />
<br />..........
<br />
<br />..........
<br />
<br />I found that for example the word "c" in atom name
"BBc" comes from
"COI" means coil. so I added manually such these words to my
1UBQ-cg.pdb file acording to 1ubq.itp file. but then again the same
warnings. Please help me with these too many warnings.
<br />
<br />7. I used -maxwarn, but when I used the command "mdrun"
the message like this appears:
<br />
<br /> Back Off! I just backed up md.log to ./#md.log.3#
<br />Getting Loaded...
<br />Reading file topol.tpr, VERSION 4.0.7 (single precision)
<br />Loaded with Money
<br />
<br />
<br />Back Off! I just backed up traj.trr to ./#traj.trr.1#
<br />
<br />Back Off! I just backed up traj.xtc to ./#traj.xtc.1#
<br />
<br />Back Off! I just backed up ener.edr to ./#ener.edr.1#
<br />starting mdrun 'protein'
<br />5000 steps, 200.0 ps.
<br />Step 0, time 0 (ps) LINCS WARNING
<br />relative constraint deviation after LINCS:
<br />rms 0.063064, max 0.267666 (between atoms 46 and 47)
<br />bonds that rotated more than 30 degrees:
<br /> atom 1 atom 2 angle previous, current, constraint length
<br /> 145 146 47.6 0.2741 0.2693 0.2700
<br /> 146 147 35.9 0.2740 0.2662 0.2700
<br /> 46 47 103.9 0.2600 0.3296 0.2600
<br /> 92 93 48.3 0.3100 0.3100 0.3100
<br /> 115 116 101.4 0.2600 0.3164 0.2600
<br />step 0
<br />Step 1, time 0.04 (ps) LINCS WARNING
<br />relative constraint deviation after LINCS:
<br />rms 241.839513, max 1323.171997 (between atoms 115 and 116)
<br />bonds that rotated more than 30 degrees:
<br /> atom 1 atom 2 angle previous, current, constraint length
<br /> 145 146 42.0 0.2693 0.2674 0.2700
<br /> 145 147 31.4 0.2759 0.2727 0.2700
<br /> 46 47 90.9 0.3296 16.2862 0.2600
<br /> 48 49 106.0 0.3100 1.1217 0.3100
<br /> 92 93 48.1 0.3100 0.3100 0.3100
<br /> 115 116 90.0 0.3164 344.2847 0.2600
<br />
<br />Back Off! I just backed up step1b.pdb to ./#step1b.pdb.1#
<br />
<br />Back Off! I just backed up step1c.pdb to ./#step1c.pdb.1#
<br />Wrote pdb files with previous and current coordinates
<br />Segmentation fault
<br />
<br />Does this error relate to too many warnings of atom names mismatching?
<br />
<br />I changed the lincs_warnangle to 90 degrees but the same massage
appeared.
<br />
<br />Thank you in advance
<br />
<br />Kargar<br />--
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