[gmx-users] Gromacs QM-MM Tutorial

Praveen Agrawal praveen at scfbio-iitd.res.in
Mon Apr 6 13:04:48 CEST 2009

Hi Dr.Groenh,
Thankyou for sharing the tutorials on QMMM capabilities of Gromacs, I am
following the same to be able to study cys-cys dimerization for short
membrane peptide. While following the tutorial I am getting errors and am
unable to find any other details to overcome it, kindly help:

1. ERROR 1 virtual site CD (Res DAT-1) has non-zero mass 12.011
   The 'trick' to create avoid virtual-virtual constraint treats atom 7 as
virtual which is 'real' atom and has non zero mass. To overcome it I
2. 32 as combination of 7 &1 and 33 as combination of 16 & 14 but that
leads to the error: Cannot have constraint (32-33) with virtual site (32)

I am using Gromacs 4.0.3 and also attaching the corresponding file for
reference. Also, would want to have your opinion on: Is attempting QM/MM
for cys-cys dimerization for short membrane peptide (25 amino acids long
each) too far fetch idea?

Best Regards,
-------------- next part --------------
A non-text attachment was scrubbed...
Name: create_tops.scr
Type: application/divxplayer-plugin
Size: 5276 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090406/471b5d7d/attachment.bin>

More information about the gromacs.org_gmx-users mailing list