[gmx-users] pdb2gmx ffG43a1 force field

Fri Oct 17 22:53:58 CEST 2014

All are from same residue.

I added following part in .rtp file.

[ BTC ]
  [ atoms ]
  Cu  Cu      1.098        0
  OA   O      -0.665       0
  OB   O      -0.665       0
  CA   C       0.778       0
  CB   C      -0.092       0
  CC   C      -0.014       0
  HM   H       0.109       0
 [ bonds ]
 Cu   OA  gb_101
 Cu   OB  gb_101
 OA   CA  gb_102
 OB   CA  gb_102
 CA   CB  gb_103
 CB   CC  gb_104
 CC   HM  gb_105
 [ angles ]
 OA   Cu   OA   ga_101
 OB   Cu   OB   ga_101
 OA   Cu   OB   ga_102
 Cu   OA   CA   ga_103
 Cu   OB   CA   ga_103
 OA   CA   OA   ga_104
 OB   CA   OB   ga_104
 OA   CA   OB   ga_105
 OA   CA   CB   ga_106
 OB   CA   CB   ga_106
 CA   CB   CC   ga_107
 CC   CB   CC   ga_108
 CB   CC   CB   ga_109
 CB   CC   HM   ga_110
 [ impropers ]
;  ai    aj    ak    al   gromos type
HM    CC   CB   CB   gd_103
CA    CB   CC   CC   gd_104
CB    CA   OA   OB   gd_104
CB    CA   OB   OA   gd_104

 [ dihedrals ]
;  ai    aj    ak    al   gromos type
 Cu    OA   CA   CB  gd_101
 Cu    OB   CA   CB  gd_101
 Cu    OA   CA   OB  gd_101
 Cu    OB   CA   OA  gd_101
 Cu    OA   CA   OA  gd_101
 Cu    OB   CA   OB  gd_101
 CB    CC   CB   CC  gd_101
 CA    CB   CC   CB  gd_101
 CA    CB   CC   HM  gd_101
 CC    CB   CC   HM  gd_101
 OA    CA   CB   CC  gd_102
 OB    CA   CB   CC  gd_102

>
> On 10/17/14 4:09 PM, Nilesh Dhumal wrote:
>> Hello,
>>
>> I am generating .top file using pdb2gmx and choose ffG43a1 force field
>> from the list.
>>
>> pdb2gmx is running for an hour. Here I pasted the last part appeared on
>> screen
>>
>> Select the Force Field:
>>   0: GROMOS96 43a1 force field
>>   1: GROMOS96 43a2 force field (improved alkane dihedrals)
>>   2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>>   3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>>   4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>>   5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>>   6: [DEPRECATED] Gromacs force field (see manual)
>>   7: [DEPRECATED] Gromacs force field with hydrogens for NMR
>>   8: Encad all-atom force field, using scaled-down vacuum charges
>>   9: Encad all-atom force field, using full solvent charges
>> 0
>> Opening library file /usr/share/gromacs/top/ffG43a1.rtp
>> Opening library file /usr/share/gromacs/top/aminoacids.dat
>> Opening library file /usr/share/gromacs/top/aminoacids.dat
>> WARNING: masses will be determined based on residue and atom names,
>>           this can deviate from the real mass of the atom type
>> Opening library file /usr/share/gromacs/top/atommass.dat
>> Entries in atommass.dat: 178
>> WARNING: vdwradii will be determined based on residue and atom names,
>>           this can deviate from the real mass of the atom type
>> Opening library file /usr/share/gromacs/top/vdwradii.dat
>> Entries in vdwradii.dat: 28
>> Opening library file /usr/share/gromacs/top/dgsolv.dat
>> Entries in dgsolv.dat: 7
>> Opening library file /usr/share/gromacs/top/electroneg.dat
>> Entries in electroneg.dat: 71
>> Opening library file /usr/share/gromacs/top/elements.dat
>> Entries in elements.dat: 218
>> Reading cu.gro...
>> Read 'Title', 156 atoms
>> Opening library file /usr/share/gromacs/top/xlateat.dat
>> 26 out of 26 lines of xlateat.dat converted succesfully
>> Analyzing pdb file
>> There are 1 chains and 0 blocks of water and 1 residues with 156 atoms
>>
>>    chain  #res #atoms
>>    1 '-'     1    156
>>
>> No occupancies in cu.gro
>> Opening library file /usr/share/gromacs/top/ffG43a1.atp
>> Atomtype 1
>> Cu
>>
>>
>> Could any one tell why is it taking so long time.
>>
>> Total number of atom are 156 in system.
>>
>
> Please see my reply from earlier to this same post:
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-October/092984.html
>
> -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
>
> ==================================================
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