[gmx-users] Generate topology

[afsaneh maleki]

Dear Justin

I copied all of files in oplsaa.ff folder in my working directory and
edited the atomname2type.n2t file as mentioned in before post in my working
directory.

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, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors
…………………………………………………..
I seem can't read atomname2type.n2t file from my working directory.

Thanks very much.
Afsaneh
On Fri, Jul 19, 2013 at 5:58 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/19/13 8:53 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 copied oplsaa.ff folder in my working directory
>>
>> 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
>>
>>
>>
>> But I get:
>>
>> opening force field file
>> /usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**atomname2type.n2t
>>
>> There are 23 name 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.
>>
>>
>>
>>
>>
>> How to solve my problem.
>>
>> Why do gromacs open /
>> usr/local/gromacs/share/**gromacs/top/oplsaa.ff/**atomname2type.n2t? I
>> copyied oplsaa.ff
>> folder in my working directory. Also I edited  .n2t file in my folder.
>>
>>
> Put the .n2t file in the working directory, not in an oplsaa.ff
> subdirectory.
>
> -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
>
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
>
> ==============================**====================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>