[gmx-users] CHARMM to Gromacs

[Alessandro.Maiorana at roma2.infn.it]

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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