[gmx-users] error in phosphoserine simulation during MD

Sun Jun 18 20:19:41 CEST 2017

Hi
Dear Justin

Thanks a lot for your kind answer, I applied two types of command to get
rid of the previous error

*at first*, the following command was used:

*gmx pdb2gmx -f *.pdb -o *.gro -p topol.top -ignh -water spc *

but I confronted these error

  CYS901  SG7090   1.414
  CYS905  SG7117   1.878   0.553
  HIS917 NE27208   2.452   1.582   1.615
  MET922  SD7245   2.131   1.439   1.748   1.108
  HIS931 NE27320   2.014   0.695   0.704   1.130   1.106
  HIS936 NE27361   3.612   2.415   2.199   1.312   1.982   1.758
  HIS940 NE27398   3.969   2.725   2.424   1.728   2.459   2.092   0.501
  CYS971  SG7630   1.026   1.229   1.407   2.263   2.378   1.823   3.283
  MET983  SD7740   1.738   0.970   1.084   2.500   2.163   1.428   3.104
  CYS984  SG7747   1.937   0.790   0.528   2.128   2.106   1.110   2.630
  HIS994 NE27836   3.472   2.296   2.070   3.194   2.934   2.170   3.046
 MET1004  SD7916   4.483   3.136   2.882   3.162   3.062   2.619   2.380
 MET1005  SD7924   4.155   2.821   2.611   2.564   2.513   2.212   1.744
 MET1010  SD7954   3.936   2.627   2.426   2.039   2.173   1.952   1.105
 MET1040  SD8205   2.685   1.774   1.361   2.871   3.096   2.021   3.142
 MET1043  SD8231   2.171   0.979   0.453   1.855   2.160   1.084   2.282
 HIS1047 NE28263   1.945   0.915   0.524   1.788   2.137   1.144   2.387
 HIS1048 NE28273   2.488   1.833   1.535   1.986   2.735   1.935   2.551
 MET1055  SD8325   2.644   1.858   1.598   3.206   3.182   2.193   3.529
                  HIS940  CYS971  MET983  CYS984  HIS994 MET1004 MET1005
                 NE27398  SG7630  SD7740  SG7747 NE27836  SD7916  SD7924
  CYS971  SG7630   3.537
  MET983  SD7740   3.355   1.644
  CYS984  SG7747   2.823   1.496   0.694
  HIS994 NE27836   3.136   3.261   1.783   1.782
 MET1004  SD7916   2.370   4.279   3.115   2.910   1.759
 MET1005  SD7924   1.813   3.983   3.014   2.762   2.059   0.728
 MET1010  SD7954   1.234   3.733   3.032   2.698   2.440   1.368   0.668
 MET1040  SD8205   3.179   1.945   1.521   1.055   2.046   3.269   3.268
 MET1043  SD8231   2.418   1.505   1.310   0.625   2.103   2.942   2.726
 HIS1047 NE28263   2.548   1.204   1.390   0.775   2.415   3.248   2.990
 HIS1048 NE28273   2.614   1.565   2.437   1.840   3.367   3.948   3.620
 MET1055  SD8325   3.619   2.132   1.214   1.107   1.747   3.277   3.362
                 MET1010 MET1040 MET1043 HIS1047 HIS1048
                  SD7954  SD8205  SD8231 NE28263 NE28273
 MET1040  SD8205   3.251
 MET1043  SD8231   2.551   1.017
 HIS1047 NE28263   2.765   1.171   0.343
 HIS1048 NE28273   3.258   1.818   1.297   1.071
 MET1055  SD8325   3.455   0.730   1.433   1.597   2.439
Start terminus MET-16: NH3+
End terminus ASN-157: COO-
Checking for duplicate atoms....
Now there are 1021 residues with 10670 atoms
Making bonds...
Warning: Long Bond (3044-3046 = 2.82265 nm)
Warning: Long Bond (4010-4012 = 0.607314 nm)
Warning: Long Bond (4995-4997 = 0.612655 nm)
Warning: Long Bond (9491-9493 = 0.796238 nm)
Number of bonds was 10864, now 10859
Generating angles, dihedrals and pairs...
Before cleaning: 17427 pairs

-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.5
Source code file: pgutil.c, line: 91

Fatal error:
Atom N is used in an interaction of type improper in the topology
database, but an atom of that name was not found in residue
number 3.

second:

 gmx pdb2gmx -f *.pdb -o *.gro -p topol.top -ignh -water spc -missing

so in this step, the mentioned error was solved. however after applying the
next commands such as

*gmx grompp -f ions.mdp -c *.pdb -p topol.top -o ions.tpr*

*another error was occurred:*Generated 279 of the 1225 non-bonded parameter
combinations

ERROR 1 [file topol.top, line 42200]:
  No default G96Angle types

ERROR 2 [file topol.top, line 42201]:
  No default G96Angle types

ERROR 3 [file topol.top, line 42202]:
  No default G96Angle types

ERROR 4 [file topol.top, line 51715]:
  No default G96Angle types

ERROR 5 [file topol.top, line 51716]:
  No default G96Angle types

ERROR 6 [file topol.top, line 51717]:
  No default G96Angle types

ERROR 7 [file topol.top, line 56644]:
  No default Proper Dih. types

ERROR 8 [file topol.top, line 61568]:
  No default Proper Dih. types

Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 1 [file topol.top, line 66972]:
  System has non-zero total charge: -13.645993
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.

There was 1 note

There was 1 warning

-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: grompp.c, line: 1372

Fatal error:
There were 8 errors in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

*thanks in advances for your attention *

*I am looking forward to getting your answer*

*best wishes*

*Marzieh*
-- 

*Marzieh DehghanPhD of BiochemistryInstitute of biochemistry and Biophysics
(IBB)University of Tehran, Tehran- Iran.*