[gmx-users] Potential issue using acpype to convert amber topology to gromacs

[Justin Lemkul]

On 2/14/18 9:33 AM, Easton J.W. wrote:
> Thanks Justin,
>
>
> Will this effect the interactions (both bonded and non-bonded) that these atoms have, as their atom types are not in the forcefield itp files?

Missing atom types would cause grompp to fail; you'd never get to the 
point where a simulation would be affected.

You're introducing custom atom types in the topology itself, and that's 
always legal before any [moleculetype] appears. The LJ parameters come 
from the [atomtypes] directive. Masses and charges present in that 
directive aren't used.

-Justin

>
> Kind regards,
>
>
> James
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
> Sent: 14 February 2018 14:22:11
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs
>
>
>
> On 2/14/18 7:14 AM, Easton J.W. wrote:
>> Hi,
>>
>>
>> I've used acpype to convert my prmtop and inpcrd files into gromacs format. I'm using the amber14sb forcefield.
>>
>>
>> At the top of the top file generated, is an [atomtypes] section. Most of the atoms in this section were present in the atomtypes.atp and ffnonbonded.itp so I deleted them however there were two atomtypes A2C and A3C that were not, so I left them.
>>
>>
>> Looking back at my files after running some simulations I have realised that these were meant to be the 2C and 3C atomtypes, which had been converted. I've also realised that they do not have any mass in the atomtypes section.
>>
>>
>> ---
>>
>>
>> [ atomtypes ]
>> ;name   bond_type     mass     charge   ptype   sigma         epsilon       Amb
>>    A2C      A2C         0.00000  0.00000   A     3.39967e-01   4.57730e-01 ; 1.91  0.1094
>>    A3C      A3C         0.00000  0.00000   A     3.39967e-01   4.57730e-01 ; 1.91  0.1094
>>
>> [ moleculetype ]
>> ;name            nrexcl
>> Peptide           3
>>
>> [ atoms ]
>> ;   nr  type  resi  res  atom  cgnr     charge      mass       ; qtot   bond_type
>>        1    N     1   CYS     N    1    -0.415700     14.01000 ; qtot -0.416
>>        2    H     1   CYS     H    2     0.271900      1.00800 ; qtot -0.144
>>        3   CX     1   CYS    CA    3     0.021300     12.01000 ; qtot -0.123
>>        4   H1     1   CYS    HA    4     0.112400      1.00800 ; qtot -0.010
>>        5  A2C     1   CYS    CB    5    -0.123100     12.01000 ; qtot -0.133
>>        6   H1     1   CYS   HB2    6     0.111200      1.00800 ; qtot -0.022
>>        7   H1     1   CYS   HB3    7     0.111200      1.00800 ; qtot 0.089
>>        8   SH     1   CYS    SG    8    -0.311900     32.06000 ; qtot -0.223
>>        9   HS     1   CYS    HG    9     0.193300      1.00800 ; qtot -0.029
>>       10    C     1   CYS     C   10     0.597301     12.01000 ; qtot 0.568
>>       11    O     1   CYS     O   11    -0.567901     16.00000 ; qtot -0.000
>>
>> ---
>>
>> What will this mean for the simulations that I have run?
> The mass and charge information will be taken from [atoms], which always
> over-writes [atomtypes] for those quantities. So there should be no
> physical problem, e.g. from a "massless" atom. You can verify the masses
> by using gmx dump on your .tpr file and checking that they're non-zero
> for those atoms, but grompp would have failed before that point if they
> were truly massless.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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