[gmx-users] error with x2top.
elie.moujaes at hotmail.co.uk
Tue Sep 25 23:02:04 CEST 2012
Thanks for your reply. I guess either way (x2top or pdb2gmx), I have problems. pdb2gmx is giving the same old error residue 'UNK' is not found in topology residue file whereas strangely enough x2top did not complain and was able to assign topologies for 73 atoms out of 94 so maybe it is easier to use x2top because in the other case I have to change files and I have no experience in this whatsoever and I am really tight on time. What do you personally think?
> Date: Tue, 25 Sep 2012 16:32:33 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] error with x2top.
> On 9/25/12 4:28 PM, Elie M wrote:
> > Dear all,
> > i am trying to convert a .gro file into a top file using .x2top but not all atoms can be assigned forcefields and the code stops with the error:
> > Generating bonds from distances...atom 94Can not find forcefield for atom C-2 with 2 bondsCan not find forcefield for atom S-3 with 0 bondsCan not find forcefield for atom C-4 with 2 bondsCan not find forcefield for atom C-7 with 3 bondsCan not find forcefield for atom C-10 with 3 bondsCan not find forcefield for atom S-12 with 0 bondsCan not find forcefield for atom C-13 with 2 bondsCan not find forcefield for atom C-16 with 2 bondsCan not find forcefield for atom O-17 with 2 bondsCan not find forcefield for atom O-18 with................Fatal error:Could only find a forcefield type for 73 out of 94 atoms
> > I looked at the .atp and n2t files. I am not sure where to start. is the second column partial charges? how to determine these? are they automatically determined ..what about the numbers at the end after each atom symbol? Is there any clear examples of how to do this? Any help would be appreciated. Thanks
> The format is explained in full here:
> The charges and atom types are determined by parameterizing the molecule of
> interest, but if you're going to do that much work, it's probably simpler to
> create an .rtp entry and have pdb2gmx do the work. g_x2top is usually intended
> to create simple topologies for simple molecules.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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