Re: NAMD FEP - Bad Hydrogen group size

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Dec 07 2011 - 06:54:01 CST

Hi John,

The problem with your setup, I suspect, is that hydrogens H4 and H5
share two parent atoms (C2 and C3), so they belong to two different
hydrogen groups (or one group containing two heavy atoms).

Here are two options:

1) duplicate atoms H4 and H5

2) make things simpler: define separate, complete topologies for both
molecules, and enforce two distance restraints linking heavy atoms
that you want to keep superimposed during the FEP transformation (see
collective variables in the user's guide). Thanks to the restraints,
this should be numerically just as efficient as the version with
shared atoms.

Also, your files indicate that you are modeling ethanol rather than methanol.

Cheers,
Jerome

On 7 December 2011 12:38, John Baker <pcxjb3_at_nottingham.ac.uk> wrote:
> Hello,
>
> I have been using NAMD for a while, but I have recently began using the FEP
> module to measure free energy differences of molecules in solvents.
>
> I am looking at the alchemical transformation of methanol --> ethane in
> water.
>
> The problem I am having is that the methanol carbon changes charge from
> 0.265 to 0, and therefore I need to include three carbon atoms.
> I placed two carbon atoms in the pdb with the same coordinates, but with
> different charges (C2, C3).
>
> Below is the PDB and PSF for the transformation in a vacuum.
>
> ATOM    1  C1  LIG     1       0.000   0.000   0.000  1.00  0.00           C
> ATOM    2  C2  LIG     1       0.000   0.000   1.530  1.00  0.00           C
> ATOM    3  H1  LIG     1       1.026   0.000 -0.373  1.00  0.00           H
> ATOM    4  H2  LIG     1     -0.512   0.888 -0.373  1.00  0.00           H
> ATOM    5  H3  LIG     1     -0.513 -0.888 -0.373  1.00  0.00           H
> ATOM    6  H4  LIG     1       0.513   0.888   1.903  1.00  0.00           H
> ATOM    7  H5  LIG     1       0.512 -0.888   1.903  1.00  0.00           H
> ATOM    8  O1  LIG     1     -1.344   0.000   2.019  1.00  0.00           O
> ATOM    9  H6  LIG     1     -1.677   0.019   2.919  1.00  0.00           H
> ATOM  10  C3  LIG     1       0.000   0.000   1.530  1.00  0.00           H
> ATOM  11  H7  LIG     1     -1.025   0.000   1.903  1.00  0.00           H
> END
>
>      11 !NATOM
>       1 O1   1    LIG  C1   CR         0.000000       12.0110           0
>       2 O1   1    LIG  C2   CR         0.265000       12.0110           0
>       3 O1   1    LIG  H1   HCMM   0.000000        1.0079           0
>       4 O1   1    LIG  H2   HCMM   0.000000        1.0079           0
>       5 O1   1    LIG  H3   HCMM   0.000000        1.0079           0
>       6 O1   1    LIG  H4   HCMM   0.000000        1.0079           0
>       7 O1   1    LIG  H5   HCMM   0.000000        1.0079           0
>       8 O1   1    LIG  O1   OR       -0.700000       15.9994           0
>       9 O1   1    LIG  H6   HOR      0.435000        1.0079           0
>     10 O1  1     LIG  C3   CR         0.000000       12.0110           0
>     11 O1  1     LIG  H7   HCMM   0.000000        1.0079           0
>
>      12 !NBOND: bonds
>       1       2       2       6       2       7       2       8
>       3       1       4       1       5       1       8       9
>      10       1      10       6      10       7      10      11
>
> When I run the simulation I receive an error of bad hydrogen group size on
> atom 2, although atom 2 is the methanol carbon and is connected to 1C, H4,
> H5 and O1.
>
> Please advise, I can't see anything wrong with the hydrogen counts.
>
> Many thanks in advance,
> John Baker (PhD candidate, University of Nottingham)
>
>
> This message and any attachment are intended solely for the addressee and
> may contain confidential information. If you have received this message in
> error, please send it back to me, and immediately delete it.   Please do not
> use, copy or disclose the information contained in this message or in any
> attachment.  Any views or opinions expressed by the author of this email do
> not necessarily reflect the views of the University of Nottingham.
>
> This message has been checked for viruses but the contents of an attachment
> may still contain software viruses which could damage your computer system:
> you are advised to perform your own checks. Email communications with the
> University of Nottingham may be monitored as permitted by UK legislation.
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:35 CST