[gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

[Venkat Reddy]

Dear all,
I am simulating a Protein-Drug complex. I am following Justin's tutorial. I
have used *PRODRG *for generating topology. *Gaussian *has given me the ESP
charges. I have edited the charges in the itp file using the *Gaussian*'s
ESP charges*. *Then I am getting this strange error.

 *ERROR 1 [file protein.top, line 75]:*
*  atom C4 (Res ORP-1) has mass 0*
*
*
*
*
*
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*ERROR 2 [file protein.top, line 75]:*
*  atom C14 (Res ORP-1) has mass 0*

But itp file has corresponding masses for both *C14 *and *C4.*
*
*
My itp file is
*
*
[ moleculetype ]
; Name nrexcl
ORP      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1         F     1  ORP      F4     1   -0.203  18.9984
     2      CCl4     1  ORP     C23     1    0.727  12.0110
     3         F     1  ORP      F5     1   -0.213  18.9984
     4         F     1  ORP      F6     2   -0.230  18.9984
     5         C     1  ORP     C21     2   -0.123  12.0110
     6       CR1     1  ORP     C22     2   -0.096  12.0110
     7        HC     1  ORP     H9Q     2    0.100   1.0080
     8       CR1     1  ORP     C20     2   -0.049  12.0110
     9        HC     1  ORP     H20     2    0.061   1.0080
    10         C     1  ORP     C19     2   -0.112  12.0110
    11      CCl4     1  ORP     C24     2    0.746  12.0110
    12         F     1  ORP      F8     2   -0.220  18.9984
    13         F     1  ORP      F9     3   -0.221  18.9984
    14         F     1  ORP      F7     3   -0.226  18.9984
    15       CR1     1  ORP     C18     3   -0.153  12.0110
    16        HC     1  ORP     H18     3    0.079   1.0080
    17         C     1  ORP     C17     3    0.161  12.0110
    18       CH2     1  ORP     C16     3    0.086  14.0270
    19         N     1  ORP      N2     3   -0.612  14.0067
    20         C     1  ORP     C25     3    0.846  12.0110
    21         O     1  ORP      O3     4   -0.449  15.9994
    22        OA     1  ORP      O4     4   -0.299  15.9994
    23       CH3     1  ORP     C26     4    0.142  15.0350
    24       CH2     1  ORP      C5     4    0.354  13.0190
    *25       CH1     1  ORP      C4     4   -0.024  14.0270*
    26       CH2     1  ORP      C3     4    0.268  13.0190
    27       CH2     1  ORP      C2     4    0.066  14.0270
    28       CH3     1  ORP      C1     5   -0.073  15.0350
    29         C     1  ORP      C6     5   -0.194  12.0110
    30       CR1     1  ORP      C7     6    0.075  12.0110
    31        HC     1  ORP      H7     6    0.005   1.0080
    32         C     1  ORP      C8     6   -0.168  12.0110
    33      CCl4     1  ORP     C15     6    0.711  12.0110
    34         F     1  ORP      F2     6   -0.214  18.9984
    35         F     1  ORP      F3     6   -0.208  18.9984
    36         F     1  ORP      F1     6   -0.215  18.9984
    37       CR1     1  ORP      C9     7   -0.030  12.0110
    38        HC     1  ORP      H9     7    0.066   1.0080
    39       CR1     1  ORP     C10     7   -0.146  12.0110
    40        HC     1  ORP     H10     7    0.094   1.0080
    41         C     1  ORP     C11     7    0.340  12.0110
    42        NR     1  ORP      N1     7   -0.647  14.0067
    43         C     1  ORP     C12     7    0.843  12.0110
    44         O     1  ORP      O1     7   -0.409  15.9994
    45        OA     1  ORP      O2     8   -0.466  15.9994
    46       CH2     1  ORP     C13     8    0.292  14.0270
    *47       CH3     1  ORP     C14     9   -0.064  15.0350*

Thanks for your valuable time
-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036