On 4/28/20 11:52 AM, Sadaf Rani wrote:
Dear Gromacs users
I am facing a problem between different versions of gromacs for gmx
pdb2gmx. I have a protein-ligand system, I did all the necessary steps
mentioned in gromacs manual for adding new residue to force field. When I
run this in gromacs 2019 it gives me a warning as below:-
Fatal error:
Invalid atomtype format: ''
But it still generates a gro file and topology. But When I am using gromacs
2020, I get the same message of invalid atomtype format as below:-

Reading 78I-T.pdb...
WARNING: all CONECT records are ignored
Read '', 4083 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
WARNING: Chain identifier 'A' is used in two non-sequential blocks.
They will be treated as separate chains unless you reorder your file.
There are 2 chains and 0 blocks of water and 492 residues with 4083 atoms

   chain  #res #atoms
   1 'A'   489   3971
   2 'A'     3    112

All occupancies are one
Opening force field file ./amber99sb-ildn.ff/atomtypes.atp

-------------------------------------------------------
Program:     gmx pdb2gmx, version 2020-UNCHECKED
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 98)

Fatal error:
*Invalid atomtype format: ''*

I am unable to sort out this problem.
I have added the atom types of my molecule as mentioned:-

;[ atomtypes ]
; name   bond_type       mass      charge    ptype      sigma      eps
       nh 14.01000     0.000       A     3.25000e-1   7.11280e-1
       hn  1.00800     0.000       A     1.06908e-1   6.56888e-2
       ca 12.01000     0.000       A     3.39967e-1   3.59824e-1
       nb 14.01000     0.000       A     3.25000e-1   7.11280e-1
       h5  1.00800     0.000       A     2.42146e-1   6.27600e-2
       nc 14.01000     0.000       A     3.25000e-1   7.11280e-1
       cd 12.01000     0.000       A     3.39967e-1   3.59824e-1
       na 14.01000     0.000       A     3.25000e-1   7.11280e-1
       c3 12.01000     0.000       A     3.39967e-1   4.57730e-1
       h2  1.00800     0.000       A     2.29317e-1   6.56888e-2
       os 16.00000     0.000       A     3.00001e-1   7.11280e-1
       h1  1.00800     0.000       A     2.47135e-1   6.56888e-2
       p5 30.97000     0.000       A     3.74177e-1   8.36800e-1
        o 16.00000     0.000       A     2.95992e-1   8.78640e-1
       oh 16.00000     0.000       A     3.06647e-1   8.80314e-1
       ho  1.00800     0.000       A     0.00000e+0   0.00000e+0
       h4  1.00800     0.000       A     2.51055e-1   6.27600e-2
        c 12.01000     0.000       A     3.39967e-1   3.59824e-1
        n 14.01000     0.000       A     3.25000e-1   7.11280e-1
       ha  1.00800     0.000       A     2.59964e-1   6.27600e-2

Could you please help me to sort out this problem. Even when the format is
incorrect does it mean that gromacs 2019 is generating a wrong topology?

You should upload a complete test case (including all force field files and your PDB structure) somewhere so that we can take a look at it. This is a weird error to try to debug. Make sure you're only ever using a plain-text editor like VIM or Emacs to avoid inclusion of inappropriate characters.

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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