[gmx-users] CHARMM to Gromacs

[Nicolas Sapay]

I add a similar problem a while ago. Unfortunately, I don't remember 
well what I have done to fix it. I think it was a stupid format problems 
like a blank line. I think I sent a message to mailing-list about that, 
without specifying it was for CHARMM, though. Here is my own version of 
NH3+ which works perfectly (my nomenclature is slightly different than 
yours) :

[ NTER ]
; standard N-terminus
; use in generate statement
;         HT1
;     (+)/
; --CA--N--HT2
;   |    \
;   HA    HT3

[ replace ]
;old_name   new_name   new_type   new_mass   new_charge
N                      NH3        14.0027    -0.30
CA                     CT1        12.0110     0.21
HA                     HB         1.0080      0.10

[ add ]
;H_added  H_catg  name   i    j    k    l
 3         4       HT     N    CA   C
;atom_type   mass     charge
 HC          1.0080    0.33

[ delete ]
HN

[ bonds ]
;   i    j    k    l
  HT1    N
  HT2    N
  HT3    N

[ dihedrals ]
;   i    j    k    l
  HT1    N   CA    C


Alessandro.Maiorana at roma2.infn.it wrote:
> Hi,
> this is a new file ffcharmm-n.tdb.
> [ None ]
>
> [ NH3+ ]
> [ replace ]
> N		NH3	14.0027	-0.3000
> CA		CT1	12.0110	0.2100
> HA		HB	1.0080	0.1000
> [ add ]
> 3	4	HT	N	CA	C
> 	HT	1.0080	0.3300
> [ delete ]
> H
>
> [ GLY-NH3+ ]
> [ replace ]
> N		NH3	14.0027	-0.3000
> CA		CT2	12.0110	0.1300
> HA1		HB	1.0080	0.0900
> HA2		HB	1.0080	0.0900
> [ add ]
> 3	4	HT	N	CA	C
> 	HT	1.0080	0.3300
> [ delete ]
> H
>
> [ NH2 ]
> [ replace ]
> N		NH3	14.0027	-0.7800
> CA		CT1	12.0110	0.0700
> HA		HB	1.0080	0.0900
> [ delete ]
> H
> [ add ]
> 2	4	HT	N	CA	C
> 	HT	1.0080	0.3100
>
>
>   
>> Alessandro.Maiorana at roma2.infn.it wrote:
>>     
>>> Hi,
>>> I'm a physics' student of Tor Vergata university(Rome). I exploit
>>> Gromacs
>>> by short time. I am trying to use the CHARMM27 force field to Gromacs,
>>> but
>>> I have some problems. I readed your instructions from web address:
>>> http://www.gromacs.org/component/option,com_docman/task,doc_details/gid,59/.
>>>
>>> I followed the procedure, that is:
>>> Step one: I converted CHARMM force field in ffcharmmbon.itp and
>>> ffcharmmnb.itp, through the use of the script
>>> "convert_charmm_to_gromacs.pl".
>>> Step two: I placed ffcharmmbon.itp and ffcharmmnb.itp in
>>> /usr/local/gromacs/share/gromacs/top.
>>> Step three: I downloaded the charmm_gromacs.tar.gz.
>>> Step four: I copied all files in the tar-file to
>>> /usr/local/gromacs/share/gromacs/top.
>>> Step five: I added this line "ffcharmm CHARMM 27" in FF.dat.
>>> Step six: The 'pdb2gmx' command was run using the command:
>>> "pdb2gmx -ter -f <filename>.pdb -o <filename>.gro -p <filename>.top" but
>>> the following error message is coming:
>>> Program pdb2gmx, VERSION 3.3.3
>>> Source code file: ter_db.c, line: 85
>>>
>>> Fatal error:
>>> Reading Termini Database: expected 3 items of atom data in stead of 1 on
>>> line
>>>        N      NH3        14.0027    -0.3000
>>>
>>> I changed the format of ffcharmm-n.tdb comparing with the ffG43a1-n.tdb,
>>> but the following error message is coming:
>>> Program pdb2gmx, VERSION 3.3.3
>>> Source code file: ter_db.c, line: 257
>>>
>>> Fatal error:
>>> Reading Termini Database: Expecting a header at line
>>>
>>>
>>>       
>> Can you show us the new format of your ffcharmm-n.tdb file?  I recall
>> having to make some changes to mine, and I suppose you've probably just
>> made a typo somewhere.  If you can paste the first entry or two of the
>> .tdb file that would help.
>>
>> -Justin
>>
>>     
>>> Can you help me? I hope to have been clear. Thanks for the help you
>>> going
>>> to gave me. See you soon.
>>>
>>>
>>>
>>>
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>>>       
>> --
>> ========================================
>>
>> 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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>>     
>
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