[gmx-users] pdb2gmx ffG43a1 force field

Justin Lemkul jalemkul at vt.edu
Fri Oct 17 22:58:06 CEST 2014 


On 10/17/14 4:53 PM, Nilesh Dhumal wrote:
> 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
>

If this is the case, your input file doesn't make any sense.  You've defined a 
single BTC residue has having 7 atoms, but your input file specifies one residue 
with 156 atoms.  Given that 156 is not evenly divisible by 7, something is wrong 
either in the .rtp or the input coordinates.

You'll need to describe in much greater detail what exactly you're working on, 
and provide (at least) your coordinate file for download.

-Justin

>
>
>
>>
>> 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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>
>

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

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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