[gmx-users] Warning: atom names in CG topology file and CG pdb file do not match

Sun Feb 6 17:40:25 CET 2011

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Dear All

I searched my problem in users mailing list but I could not find the
answer. please help me with this.
I am learning the CG Martini force
filed using the tutorial
"protein in water" for protein ubiquitin. so I did the things like
below:

1. awk -f atom2cg_v2.1.awk 1UBQ.pdb > 1UBQ-cg.pdb (it makes a CG
.pdb file)

2. wget ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt

3. grep -A 1 1ubq pdb_seqres.txt > 1ubq.seq (these 2 and 3
commands make a .seq file)

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.)

5. I make a 1ubq.top file like below

#include "martini_v2.1.itp"

#include "1ubq.itp"

[ system ]

; name

protein

[ molecules ]

; name  number

protein 1

6. grompp -f 1ubq.mdp -c 1UBQ-cg.pdb -p 1ubq.top

but warnings come like this

Warning: atom name 1 in 1ubq.top and 1UBQ-cg.pdb does not match (BBc
- BB)

Warning: atom name 2 in 1ubq.top and 1UBQ-cg.pdb does not match (S1c
- S1)

Warning: atom name 3 in 1ubq.top and 1UBQ-cg.pdb does not match (BBe
- BB)

............

............

all of my atom names mismatch. I checked the 1ubq.itp. some lines
are in below

;;; MARTINI 2.1 coarse-grained topology

;;; Generated by seq2itp.pl version 1.1.4

;;; SEQ: MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL  50

;;; SEQ: EDGRTLSDYN IQKESTLHLV LRLRGG

;;; Total Number of Amino Acid Residues: 76

[moleculetype]

;molname    exclusions

Protein    1

[atoms]

1    Qd    1    MET    BBc    1    1.000    ;    COI

2    C5    1    MET    S1c    2    0.000    ;    COI

3    Nda    2    GLN    BBe    3    0.000    ;    EXT

........

........

[ bonds ]

;backbone-backbone bonds

1    3    1    0.350    400    ;    COI-EXT

3    5    1    0.350    1250    ;    EXT-EXT

5    7    1    0.350    1250    ;    EXT-EXT

........

........

[ constraints ]

;sc-sc constraints (Ring Structures)

8    9    1    0.270    ;    PHE4

8    10    1    0.270    ;    PHE4

9    10    1    0.270    ;    PHE4

.........

.........

[angles]

;backbone-backbone-backbone angles

1    3    5    2    127.00    25    ;    COI-EXT-EXT

3    5    7    2    134.00    25    ;    EXT-EXT-EXT

5    7    11    2    134.00    25    ;    EXT-EXT-EXT

.............

.............

[dihedrals]

;improper dihedral angles

7    9    10    8    2    0.00    50    ;    PHE4

94    96    97    95    2    0.00    50    ;    PHE45

..........

..........

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.

7. I used -maxwarn, but when I used the command "mdrun"
the message like this appears:

  Back Off! I just backed up md.log to ./#md.log.3#

Getting Loaded...

Reading file topol.tpr, VERSION 4.0.7 (single precision)

Loaded with Money

Back Off! I just backed up traj.trr to ./#traj.trr.1#

Back Off! I just backed up traj.xtc to ./#traj.xtc.1#

Back Off! I just backed up ener.edr to ./#ener.edr.1#

starting mdrun 'protein'

5000 steps,    200.0 ps.

Step 0, time 0 (ps)  LINCS WARNING

relative constraint deviation after LINCS:

rms 0.063064, max 0.267666 (between atoms 46 and 47)

bonds that rotated more than 30 degrees:

 atom 1 atom 2  angle  previous, current, constraint length

    145    146   47.6    0.2741   0.2693      0.2700

    146    147   35.9    0.2740   0.2662      0.2700

     46     47  103.9    0.2600   0.3296      0.2600

     92     93   48.3    0.3100   0.3100      0.3100

    115    116  101.4    0.2600   0.3164      0.2600

step 0

Step 1, time 0.04 (ps)  LINCS WARNING

relative constraint deviation after LINCS:

rms 241.839513, max 1323.171997 (between atoms 115 and 116)

bonds that rotated more than 30 degrees:

 atom 1 atom 2  angle  previous, current, constraint length

    145    146   42.0    0.2693   0.2674      0.2700

    145    147   31.4    0.2759   0.2727      0.2700

     46     47   90.9    0.3296  16.2862      0.2600

     48     49  106.0    0.3100   1.1217      0.3100

     92     93   48.1    0.3100   0.3100      0.3100

    115    116   90.0    0.3164 344.2847      0.2600

Back Off! I just backed up step1b.pdb to ./#step1b.pdb.1#

Back Off! I just backed up step1c.pdb to ./#step1c.pdb.1#

Wrote pdb files with previous and current coordinates

Segmentation fault

Does this error relate to too many warnings of atom names mismatching?

I changed the lincs_warnangle to 90 degrees but the same massage
appeared.

Thank you in advance

Kargar

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