[gmx-users] atom name not match
Yu Sun
yus at CLEMSON.EDU
Fri Jan 2 20:32:01 CET 2004
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
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