[gmx-users] OPLS-AA Unknown Atomtype

Yao Yao yao0o at ymail.com
Mon Aug 29 08:59:40 CEST 2011 

Hi Justin,

Thanks for your last reply. Now it seems that OPLS has known the atomtypes after I added those CA1, ... to ffoplsaanb.itp,
but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it still gives errors like,

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
checking input for internal consistency...
processing topology...
Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp
Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp
Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp
Generated 338253 of the 338253 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 338253 of the 338253 1-4 parameter combinations

ERROR 1 [file cro.top, line 37]:
  No default Bond types


ERROR 2 [file cro.top, line 71]:
  No default Angle types


ERROR 3 [file cro.top, line 72]:
  No default Angle types


ERROR 4 [file cro.top, line 85]:
  No default Angle types


ERROR 5 [file cro.top, line 91]:
  No default Ryckaert-Bell. types


ERROR 6 [file cro.top, line 92]:
  No default Ryckaert-Bell. types


ERROR 7 [file cro.top, line 93]:
  No default Ryckaert-Bell. types


ERROR 8 [file cro.top, line 108]:
  No default Ryckaert-Bell. types


ERROR 9 [file cro.top, line 112]:
  No default Proper Dih. types


ERROR 10 [file cro.top, line 113]:
  No default Proper Dih. types


ERROR 11 [file cro.top, line 114]:
  No default Proper Dih. types

Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp
Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 1 [file cro.top, line 142]:
  System has non-zero total charge: -1.022478e+00
  


processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...

There was 1 note

-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: grompp.c, line: 986

Fatal error:
There were 11 errors in input file(s)
-----------------------------------------------

I do double-check those bondtypes, angles, and interactions mentioned in the errors, and I am pretty sure I have already declared those values in the ffoplsaabon.itp. 
Is there any other file I also need to mention those values?

Thanks,

Yao













________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, August 23, 2011 2:07 PM
Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype



Yao Yao wrote:
> Hi Justin,
> 
> Thanks for your reply. Here is the exact error message,
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> processing topology...
> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp
> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp
> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp
> 
> -------------------------------------------------------
> Program grompp, VERSION 4.0.7
> Source code file: toppush.c, line: 620
> 
> Fatal error:
> Unknown bond_atomtype CA1
> 
> -------------------------------------------------------
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> I understand that I have not inserted CA1 into "atomtypes.atp". because if I add CA1 as a new atom, I have to mention all bonds, angles, dihedrals of it.

The atomtypes.atp file is irrelevant here; it is only used by pdb2gmx.  What you are trying to avoid is what you have to do - if you introduce a new atom type and intend to use it in any bonded interactions, you must introduce relevant parameters for all the interactions in which it will participate.

> So I denoted the type of it as a known carbon atom in my topology file (in the attachment). I thought in OPLS-AA, CA1 can "cite" this known atom since CA1 is just a name.

Names and types are different.  You can name an atom anything you like, but atom types must be judiciously assigned.

> Meanwhile, in the ffbonded.itp and ffnonbonded.itp, I still use CA1 to give bonds, angles, and dihedrals of CA1.
> 

If you have inserted all of the correct parameters in these files, you would not receive the error above.  Perhaps herein lies the problem - if you have modified ffnonbonded.itp (which belongs to the force field organization of the 4.5.x series), it will have no effect on a 4.0.7 executable, which is being called above.  So (at least) one of two possibilities is true:

1. You're not using the Gromacs version you intend to.
2. You haven't introduced all of the parameters you need to.

The bond_atomtype values are assigned in ffnonbonded.itp (counterintuitive, I know, but that's how it works).  So for the problematic atom (type opls_137) the bond_atomtype is CT (second column of ffnonbonded.itp in [atomtypes]).

> So generally speaking, I am wondering if an atom with a different name gets introduced into OPLS, it has to be denoted again (bonds, angles, ...) and added into the atomtypes.atp, even it is a carbon atom?
> And do you happen to know any tutorial about how to introduce new molecules into OPLS?
> 

Again, names are irrelevant but types are critical.  There is no tutorial, per se, but the instructions are on the wiki in a general form:

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

Most of the instructions are designed around residues for which pdb2gmx will act.  In your case, any new atom types need to be defined in ffnonbonded.itp and then bonded interactions making use of those types in ffbonded.itp.

-Justin

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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