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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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