[gmx-users] atom name not match

[Yu Sun]

Dear gmx-users,

I am modelling a SAM surface and want to do energy minimization. The SAM is 
consisted of two types of chains: OH-terminated chain and COO- -terminated. 
Therefore, I created two .itp files for each type and in the .top file 
included these .itp files. The final system consisted of 55 COO- termianted 
chains , 458 OH-terminated chains, and 6349 water. When using grompp, I 
receive warning message as follows:


       Warning: atom names in CATP10SAM.top and CATP10SAM_b4em.gro don't 
match (O - HO)
       ...
      102 non-matching atom names
      atom names from CATP10SAM.top will be used
      atom names from CATP10SAM_b4em.gro will be ingnored


After doing energy minimization, I found in the output gro file all the OHT 
chains are replaced by CAT chains. Where I am wrong ?

Here are the files :
----------------
OHT.itp file :
------------------
; OH terminated SAM chain

[ moleculetype ]
; Name  nrexcl
OHT     3

[ atoms ]
; nr    type    resnr   residu  atom    cgnr    charge
1       CH1     1     OHT       C1      1       0.263
2       CH2     1       OHT     C2      2       0.0
3       CH2     1       OHT     C3      3       0.0
4       CH2     1       OHT     C4      4       0.0
5       CH2     1       OHT     C5      5       0.0
6       CH2     1       OHT     C6      6       0.0
7    CH2   1     OHT   C7    7     0.0
8    CH2   1     OHT   C8    8     0.0
9    CH2   1     OHT   C9    9     0.0
10   CH3   1     OHT   C10   10    0.0
11    OA   1    OHT   OA    1   -0.566
12    HO   1     OHT   HO    1     0.303

[ bonds ]
....

--------
CAT.itp file :
-----------------

; carboxly terminated SAM chain

[ moleculetype ]
; Name  nrexcl
CAT     3

[ atoms ]
; nr    type    resnr   residu  atom    cgnr    charge
1       C       1     CAT       C1      1       0.679
2       CH2     1       CAT     C2      2     -0.095
3       CH2     1       CAT     C3      3       0.0
4       CH2     1       CAT     C4      4       0.0
5       CH2     1       CAT     C5      5       0.0
6       CH2     1       CAT     C6      6       0.0
7    CH2   1     CAT   C7    7     0.0
8    CH2   1     CAT   C8    8     0.0
9    CH2   1     CAT   C9    9     0.0
10   CH3   1     CAT   C10   10    0.0
11   OA 1       CAT   OA        1       -0.792
12   O     1    CAT   O     1   -0.792

[ bonds ]
...
------------------
CATP10SAM.top file
-----------------
; The force field to be included
#include "ffgmx.itp"

; Include the CAT topology
#include "CAT.itp"

; Include the OHT topology
#include "OHT.itp"

; Include SPC Water topology
#include "spc.itp"

[ system ]
SAM  in  water

[ molecules ]
CAT               55
OHT                   458
SOL              6349

---------------------------------
A portion of CATP10SAM_b4em.gro
----------------------------------
....

   359OHT     C1 4297   8.328   1.519   7.689
   359OHT     C2 4298   8.230   1.435   7.607
   359OHT     C3 4299   8.171   1.319   7.689
   359OHT     C4 4300   8.072   1.234   7.607
   359OHT     C5 4301   8.013   1.117   7.689
   359OHT     C6 4302   7.915   1.032   7.607
   359OHT     C7 4303   7.856   0.916   7.689
   359OHT     C8 4304   7.757   0.831   7.607
   359OHT     C9 4305   7.699   0.714   7.689
   359OHT    C10 4306   7.600   0.629   7.607
   359OHT     OA 4307   8.379   1.626   7.608
   359OHT     HO 4308   8.464   1.665   7.652
   360CAT     C1 4309   8.328   1.520   8.550
   360CAT     C2 4310   8.230   1.435   8.467
   360CAT     C3 4311   8.171   1.319   8.549
   360CAT     C4 4312   8.072   1.234   8.467
   360CAT     C5 4313   8.013   1.117   8.549
   360CAT     C6 4314   7.915   1.032   8.467
   360CAT     C7 4315   7.856   0.916   8.549
   360CAT     C8 4316   7.757   0.831   8.467
   360CAT     C9 4317   7.699   0.714   8.549
   360CAT    C10 4318   7.600   0.629   8.467
   360CAT     OA 4319   8.355   1.485   8.686
   360CAT      O 4320   8.384   1.617   8.499


Thanks,



Yu Sun  (Denis)
Postdoc
Department of Bioengineering
Clemson, SC 29631
Tel. (864)656-1352
email: yus at clemson.edu