[gmx-users] N-terminal Database: ffG43a1-n.tdb

[Miguel Machuqueiro]

Hi there again,

A few day ago I posted a question but it was probably to technical and the 
developers were on Easter vacation ;o)

Anyways, here goes again the same question:

I'm having trouble modifying the file ffG43a1-n.tdb (of the termini 
databases) in order to get the NH2 section to bear an extra hydrogen (with 
mass but without charge).

The problem has to do with the way PDB2GMX deals with this database. 
Changing around (check below), this was the best I could do. Afterwards I 
change by hand the charge of H3 to 0.000.

Any ideas on how to fool PDB2GMX with this one???

This is a good one for the developers... can you help me?

Before:
_______________________________

[ NH2 ]
[ replace ]
N	N	NL	14.0067	-0.83
[ add ]
2	4	N	CA	C
	H	H	1.008	0.415
[ delete ]
H

After:
________________________________

[ NH2 ]
[ replace ]
N	N	NT	14.0067	-0.83
[ add ]
2	4	N	CA	C
	H	H	1.008	0.415
[ delete ]
H


=========================================
Miguel Machuqueiro
ITQB-Instituto de Tecnologia Química e Biológica
     Universidade Nova de Lisboa
Molecular Simulation Group - 6º Floor (Room 601)
Av. da República, EAN, Apartado 127
2781-901 Oeiras, Portugal
Tel. : +351 265 501614 /Mobile: +351 96 7562285
E-mail1: machuque at itqb.unl.pt
E-mail2: miguel.machuqueiro at ioc.unibe.ch
E-mail3: masm at fc.ul.pt
__________________________________________