[gmx-users] Partial Charge precision

[Justin Lemkul]

On 5/28/18 10:34 AM, Momin Ahmad wrote:
> Hello,
> how many decimal digits are allowed in .rtp files for partial charges?
>
> i got this error:
>
> ##########################################
> Using the Uff4mof force field in directory ./uff4mof.ff
>
> No file 'watermodels.dat' found, will not include a water model
> Reading benzene.pdb...
> Read 'BENZENE', 12 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> There are 1 chains and 0 blocks of water and 1 residues with 12 atoms
>
>   chain  #res #atoms
>   1 ' '     1     12
>
> All occupancies are one
> Opening force field file ./uff4mof.ff/atomtypes.atp
>
> Invalid format: [ atomtypes ]
> Atomtype 146
> Reading residue database... (uff4mof)
> Opening force field file ./uff4mof.ff/bb.rtp
>
> -------------------------------------------------------
> Program:     gmx pdb2gmx, version 2016.3
> Source file: src/gromacs/gmxpreprocess/resall.cpp (line 489)
>
> Fatal error:
> in .rtp file in residue BDC at line:
>     C1        C_1        -0.031398100000000005
> ###########################################
>
> I wrote down the whole number and did not round anything.
>

That's way too many digits to have any practical use or meaning. I'd 
suggest rounding to -0.0314.

The error is about the format of the line, not the precision of the 
value, so your .rtp entry is broken in some way (perhaps simply due to 
the absence of a charge group number, but it could be one of several 
things).

-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.thelemkullab.com

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