Dear Fateme,
Use ACPYPE and give prmtop and inpcrd as input it will generate
corresponding top and gro file compatible with gromacs.
Sincerely yours,
Dhaval Patel | PhD
The M. S. University of Baroda, Vadodara.
Lab: Biophysics & Structural Biology,
Indian Institute of Advanced Research,
Gujarat, INDIA. +91 9925450504
pateldhaval.in.gmail.com; dhaval.iiar.res.in
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02/20/19,
10:14:55 AM
On Wed, Feb 13, 2019 at 8:22 PM fateme haghighi <fateme.haghighi.hotmail.com>
wrote:
> Hi everyone
>
> Anyone has idea why when I converted the prmtop file in which is created
> by TLEAP to gromacs.top file, the mass and charge columns are shown zero
> values? However I have checked by gaussian out put of single point and pdb
> file. Both are the same. How can I resolve the problem?
>
> [ atomtypes ]
> ;name bond_type mass charge ptype sigma epsilon
> Amb
> CB CB 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ;
> 1.91 0.0860
> N* N* 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ;
> 1.82 0.1700
> NB NB 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ;
> 1.82 0.1700
> HC HC 0.00000 0.00000 A 2.64953e-01 6.56888e-02 ;
> 1.49 0.0157
> CT CT 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ;
> 1.91 0.1094
> N2 N2 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ;
> 1.82 0.1700
> CA CA 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ;
> 1.91 0.0860
> NC NC 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ;
> 1.82 0.1700
> CQ CQ 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ;
> 1.91 0.0860
> S S 0.00000 0.00000 A 3.56359e-01 1.04600e+00 ;
> 2.00 0.2500
> H1 H1 0.00000 0.00000 A 2.47135e-01 6.56888e-02 ;
> 1.39 0.0157
> H H 0.00000 0.00000 A 1.06908e-01 6.56888e-02 ;
> 0.60 0.0157
> HA HA 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ;
> 1.46 0.0150
> F F 0.00000 0.00000 A 3.11815e-01 2.55224e-01 ;
> 1.75 0.0610
> OS OS 0.00000 0.00000 A 3.00001e-01 7.11280e-01 ;
> 1.68 0.1700
> OH OH 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ;
> 1.72 0.2104
> HO HO 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ;
> 0.00 0.0000
>
> [ moleculetype ]
> ;name nrexcl
> UNX 3
>
> [ atoms ]
> ; nr type resi res atom cgnr charge mass ; qtot
> bond_type
> 1 CB 1 UNX C1 1 0.000000 12.01000 ; qtot 0.000
> 2 CB 1 UNX C2 2 0.000000 12.01000 ; qtot 0.000
> 3 N* 1 UNX N1 3 0.000000 14.01000 ; qtot 0.000
> 4 NB 1 UNX N2 4 0.000000 14.01000 ; qtot 0.000
> 5 NB 1 UNX N3 5 0.000000 14.01000 ; qtot 0.000
> 6 HC 1 UNX H1 6 0.000000 1.00800 ; qtot 0.000
> 7 CT 1 UNX C3 7 0.000000 12.01000 ; qtot 0.000
> 8 CT 1 UNX C4 8 0.000000 12.01000 ; qtot 0.000
> 9 N2 1 UNX N4 9 0.000000 14.01000 ; qtot 0.000
> 10 CA 1 UNX C5 10 0.000000 12.01000 ; qtot 0.000
> 11 NC 1 UNX N5 11 0.000000 14.01000 ; qtot 0.000
> 12 CQ 1 UNX C6 12 0.000000 12.01000 ; qtot 0.000
> 13 NC 1 UNX N6 13 0.000000 14.01000 ; qtot 0.000
> 14 S 1 UNX S1 14 0.000000 32.06000 ; qtot 0.000
>
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Received on Tue Feb 19 2019 - 21:00:02 PST
