On 7/19/13 9:32 AM, afsaneh maleki wrote:
Dear Justin
I want a topology for an arbitrary molecule (44 atom) and I use x2top
program that .n2t file is it’s input.
The .pdb file is as the following:
ATOM 1 O5 TPT 1 -6.131 -0.245 0.000 0.000000
ATOM 2 C21 TPT 1 -5.041 0.384 0.000 0.000000
ATOM 3 O6 TPT 1 -5.040 1.814 0.000 0.000000
ATOM 4 H12 TPT 1 -5.945 2.134 0.000 0.000000
ATOM 5 C18 TPT 1 -3.708 -0.387 0.000 0.000000
ATOM 6 C19 TPT 1 -2.374 0.383 0.000 0.000000
ATOM 7 H10 TPT 1 -2.373 1.453 0.000 0.000000
……
I edited atomname2type.n2t file is as the following:
O opls_267 -0.495284 15.9994 1 C 0.1214
C opls_470 0.594326 12.0110 3 C 0.1487 O 0.1306 O 0.1214
O opls_268 -0.560735 15.9994 2 C 0.1306 H 0.0974
H opls_270 0.417334 1.0079 1 O 0.0974
C opls_145 0.037549 12.0110 3 C 0.1487 C 0.1387 C 0.1387
C opls_145 -0.145422 12.0110 3 C 0.1387 H 0.1087 C 0.1395
H opls_146 0.110842 1.0079 1 C 0.1087
……
I used these command:
] g_x2top –f .pdb –o .top -pbc –ff oplsaa
And gromacs get me:
opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t
There are 23 names to type translations in file oplsaa.ff
Generating bonds from distances...
atom 44
Can not find forcefield for atom C21-2 with 3 bonds
Can not find forcefield for atom C18-5 with 3 bonds
Can not find forcefield for atom C16-10 with 3 bonds
Can not find forcefield for atom C20-11 with 3 bonds
Can not find forcefield for atom C15-17 with 3 bonds
Can not find forcefield for atom C12-18 with 3 bonds
Can not find forcefield for atom C7-27 with 3 bonds
Can not find forcefield for atom C5-28 with 3 bonds
Can not find forcefield for atom C3-33 with 3 bonds
Can not find forcefield for atom C2-34 with 3 bonds
Can not find forcefield for atom C9-40 with 3 bonds
Can not find forcefield for atom C10-41 with 3 bonds
Program g_x2top, VERSION 4.5.4
Source code file: g_x2top.c, line: 206
Fatal error:
Could only find a forcefield type for 32 out of 44 atoms for more
information and tips for troubleshooting,
…………………………………………………..
I copied all of files in oplsaa.ff folder in my working directory and
edited the atomname2type.n2t file as the above mentioned in my working
directory.
How to solve my problem?
Why do gromacs open /
usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t?
Let's not go backwards. I responded to this post already and you gave a cryptic
reply about some new error. Please respond to the other post.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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