[gmx-users] cant find certain atomtypes from atomtype database

[Justin Lemkul]

On 10/24/13 1:03 AM, JuYeon wrote:
> dear gromacs users
> im using gromacs to make CS2 MD programs i made pdb file (by converting mol file to pdb file) and rtp file for CS2this is what i made
> <pdb file>
> COMPND    UNNAMEDAUTHOR    GENERATED BY OPEN BABEL 2.3.2HETATM    1  C   LIG     1      19.882  -4.263  -0.027  1.00  0.00           C  HETATM    2  S   LIG     1      21.256  -5.103  -0.054  1.00  0.00           S  HETATM    3  S   LIG     1      18.508  -3.424   0.000  1.00  0.00           S  CONECT    1    2    3                                                 CONECT    2    1                                                      CONECT    3    1                                                      MASTER        0    0    0    0    0    0    0    0    3    0    3    0END
> -------------------------------------------------------------------------------------
> <rtp file>
> [ LIG ]  [ atoms ]C   opls_77	0	0S1  opls_202	0	0S2  opls_202	0	0
>   [ bonds ]C  S1C  S2
> i attached rtp file to /usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp andi added it to residuetypes.dat (which is in /usr/share/gromacs/top)then i wrote command pdb2gmx to make gro file but it failed
> Fatal error:Atom type opls_77 (residue LIG) not found in atomtype databaseFor more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors
> before i made rtp file, i checked atomtypes atp file which is in oplsaa.ff it says olps_77 is carbon(isobutene) and opls_202 is sulfides i dont know why gromacs cant find atom type opls_77

opls_77 does not exist.  opls_077 does.  The bigger problem is that you should 
probably not be mixing OPLS-UA parameters (opls_077) with OPLS-AA (opls_202).  I 
suspect a better model can be built from self-consistent parameters.

> also, to make rtp file how to give charge and charge group to each atoms?

Refer to the 2001 OPLS-AA paper for the details of the required QM calculations. 
  The charge group is simple; the whole molecule (since it is only 3 atoms) can 
be one group.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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