[gmx-users] pdb to tpr !

Swetha Vijayakrishan swetha at www.cdfd.org.in
Tue Jul 8 08:37:00 CEST 2003

hello all,

i need to convert a pdb file to the tpr format.
i thought i should go about doing it by first converting it to a top file
by "x2top" and then converting the top to tpr by the "grompp" command.

when i used the x2top command,and selected the GROMOS96 43a1
Forcefield (official distribution),i got the following error :

Select the Force Field:
 0: Gromacs Forcefield (see manual)
 1: Gromacs Forcefield with all hydrogens (proteins only)
 2: GROMOS96 43a1 Forcefield (official distribution)
 3: GROMOS96 43b1 Vacuum Forcefield (official distribution)
 4: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
Generating bonds from distances...
Opening library file /usr/local/share/gromacs/top/ffG43a1.atp
There are 46 type to mass translations
atom 6180
Opening library file /usr/local/share/gromacs/top/ffG43a1.n2t
There are 20 name to type translations
Fatal error: No forcefield type for atom CG2 (7) with 1 bonds

i'm not sure what this means as the CG1 and CG2 atomtypes are defined in
the topology file.
Would really appreciate some help on how to go about solving this.

Also i had done my MD in charmm and now i'm analysing it in GROMACS.so
in the creation of the tpr file,is the selection of the GROMOS96 43a1
field equivalent to the Charmm force field.Is this an important factor to
keep in mind during the conversion that the force fields are the same?

I would also like to know if there is any other direct way of converting
the pdb to tpr?




Swetha Vijayakrishnan

Project Assistant
C/O Dr.Shekhar.C.Mande
Centre for DNA Fingerprinting and Diagnostics(CDFD),
ECIL Road,Nacharam,
Hyderabad - 500076

Phone:: Direct: 91-040-7171442
        Indirect: 91-040-7151344/46/47/56 (lab extn 1400)

Fax  :: 91-040-(7155479-7155610>

Email:: swetha at cdfd.org.in
        swethasenorita at yahoo.com

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