[gmx-users] error in phosphoserine simulation during MD

[Justin Lemkul]

On 6/18/17 2:19 PM, marzieh dehghan wrote:
> 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)

Long bonds suggest discontinuities in the protein chain - this means missing 
atoms that have to be modeled back in.  These should be clearly indicated in the 
PDB file, as I said before.

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

Using -missing to simply bypass an error message is (almost) always an incorrect 
choice.  Only very unusual cases justify its use.  In your case, don't do it.

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

Naturally this fails because your topology is garbage:


> 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.
> 

Start over.  Find and model in the missing atoms, then try again.  Your current 
topology is unusable.

-Justin

-- 
==================================================

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

==================================================