On 10/12/16 11:06 PM, Dd H wrote:
I found these words in the GROMACS v4.5.5 manual:

*[ atoms ] : defines the molecule, where nr and type are fixed, the rest is
user defined. So*
*atom can be named as you like, cgnr made larger or smaller (if possible,
the total charge of a **charge group should be zero), and charges can be
changed here too.*

So does it means the mass and charge of [ atomtypes ] section could be
modified in [ atoms ] section?


Look at the example in section 5.7.2. Note that masses are absent. If masses are not provided in [atoms], they are referenced from [atomtypes]. Charges present in [atomtypes] are never used for anything and must be specified in [atoms].

-Justin

On 12 October 2016 at 23:30, Alan <alanwil...@gmail.com> wrote:

But read the GMX manual to understand why it's all fine.

On 12 October 2016 at 13:29, Dd H <ddhe...@gmail.com> wrote:

Thank you!

On 12 October 2016 at 19:50, Alan <alanwil...@gmail.com> wrote:

It's all fine.

On 12 October 2016 at 12:34, Dd H <ddhe...@gmail.com> wrote:

I use this command:
acpype -p filename.prmtop -x filename.inpcrd

It generates parameter files for GROMACS and my question is about the
.top
file of outputs.

On 12 October 2016 at 18:22, Alan <alanwil...@gmail.com> wrote:

Which acpype command did you specifically used?

acpype may be able to use Antechamber and calculate partial
charges.
See
acpype -h

On 12 October 2016 at 09:56, Dd H <ddhe...@gmail.com> wrote:

Hi everyone,
I generated a .top file of a ligand using acpype for MD
simulations.
There
are some new atom types in [ atomtypes ] section, but the data of
mass
and
charge columns of the section are zeros. However they can be
found
in
the [
atoms ] section. Can you tell me if this file is ok for MD
simulations?
Thank you in advance!

Dading Huang
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United Kingdom
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Wellcome Trust Genome Campus
Hinxton
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United Kingdom
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