[gmx-users] problem regarding .top file generated by genbox

[Justin A. Lemkul]

I suspect you have an error with the order that you have included the relevant
.itp files within your topology.  It would be helpful to include a snapshot of
your topology which illustrated the order in which these files are included.

Also, if you are asking whether your commands are right or not, you should
include your actual commands, otherwise our default assumption is "probably
not." :-)

-Justin

Quoting sudheer babu <sudheer.pbm07 at gmail.com>:

> HI gmxusers,
> i am using gromacs version 3.3.1
> i am new to gromocs, i was taken protein.top file (which is generated by
> pdb2gmx). In this file i have included ff.itp , popc.itp and lipid.itp but
> protein atom types already there (generated by pdb2gmx). This .top file used
> for inserting of protein into mebranes by using genbox. It was run without
> problem, given .gro which contain both protein and popc and .top file . when
> i have used this .top and .gro for energy minimisation it's showing that,
> Fatal error:
> Atom types NR, HC , CR1 not found
> these type of atoms not there in .gro file but present in .top file .
> Iam pasting the aminoacids which contain these type of atoms
>
> 17          N      3   HISH      N      7      -0.28    14.0067   ; qtot
> 0.72
>     18          H      3   HISH      H      7       0.28      1.008   ; qtot
> 1
>     19        CH1      3   HISH     CA      8          0     13.019   ; qtot
> 1
>     20        CH2      3   HISH     CB      8          0     14.027   ; qtot
> 1
>     21          C      3   HISH     CG      9      -0.05     12.011   ; qtot
> 0.95
>     22         NR      3   HISH    ND1      9       0.38    14.0067   ; qtot
> 1.33
>     23          H      3   HISH    HD1      9        0.3      1.008   ; qtot
> 1.63
>     24        CR1      3   HISH    CD2      9          0     13.019   ; qtot
> 1.63
>     25        CR1      3   HISH    CE1      9      -0.24     13.019   ; qtot
> 1.39
>     26         NR      3   HISH    NE2      9       0.31    14.0067   ; qtot
> 1.7
>     27          H      3   HISH    HE2      9        0.3      1.008   ; qtot
> 2
>     28          C      3   HISH      C     10       0.38     12.011   ; qtot
> 2.38
>     29          O      3   HISH      O     10      -0.38    15.9994   ; qtot
> 2
>     30          N      4   HISH      N     11      -0.28    14.0067   ; qtot
> 1.72
>     31          H      4   HISH      H     11       0.28      1.008   ; qtot
> 2
>     32        CH1      4   HISH     CA     12          0     13.019   ; qtot
> 2
>     33        CH2      4   HISH     CB     12          0     14.027   ; qtot
> 2
>     34          C      4   HISH     CG     13      -0.05     12.011   ; qtot
> 1.95
>     35         NR      4   HISH    ND1     13       0.38    14.0067   ; qtot
> 2.33
>     36          H      4   HISH    HD1     13        0.3      1.008   ; qtot
> 2.63
>     37        CR1      4   HISH    CD2     13          0     13.019   ; qtot
> 2.63
>     38        CR1      4   HISH    CE1     13      -0.24     13.019   ; qtot
> 2.39
>     39         NR      4   HISH    NE2     13       0.31    14.0067   ; qtot
> 2.7
>     40          H      4   HISH    HE2     13        0.3      1.008   ; qtot
> 3
>     41          C      4   HISH      C     14       0.38     12.011   ; qtot
> 3.38
>     42          O      4   HISH      O     14      -0.38    15.9994   ; qtot
> 3
>
>
>   308          N     36    PHE      N    133      -0.28    14.0067   ; qtot
> 2.72
>    309          H     36    PHE      H    133       0.28      1.008   ; qtot
> 3
>    310        CH1     36    PHE     CA    134          0     13.019   ; qtot
> 3
>    311        CH2     36    PHE     CB    134          0     14.027   ; qtot
> 3
>    312          C     36    PHE     CG    134          0     12.011   ; qtot
> 3
>    313          C     36    PHE    CD1    135       -0.1     12.011   ; qtot
> 2.9
>    314         HC     36    PHE    HD1    135        0.1      1.008   ; qtot
> 3
>    315          C     36    PHE    CD2    136       -0.1     12.011   ; qtot
> 2.9
>    316         HC     36    PHE    HD2    136        0.1      1.008   ; qtot
> 3
>    317          C     36    PHE    CE1    137       -0.1     12.011   ; qtot
> 2.9
>    318         HC     36    PHE    HE1    137        0.1      1.008   ; qtot
> 3
>    319          C     36    PHE    CE2    138       -0.1     12.011   ; qtot
> 2.9
>    320         HC     36    PHE    HE2    138        0.1      1.008   ; qtot
> 3
>    321          C     36    PHE     CZ    139       -0.1     12.011   ; qtot
> 2.9
>    322         HC     36    PHE     HZ    139        0.1      1.008   ; qtot
> 3
>    323          C     36    PHE      C    140       0.38     12.011   ; qtot
> 3.38
>    324          O     36    PHE      O    140      -0.38    15.9994   ; qtot
> 3
>
> have i given wrong command
> pls help me,
> thanks in advance.
>



========================================

Justin A. Lemkul
Graduate Research Assistant
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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