[gmx-users] How to use PRODRG to help new user do gromacs?

[Yang Ye]

What' in the bottom of drgcns.top?

On 9/6/2007 2:03 AM, Yafei Dai wrote:
> Hi, all,
> I am a new user of gromacs and I read the manual and tutorial but I still get confused.
> I need your help.
>
> >From PRODRG, I got four *.top files, one *.itp file and three *.PDB files and some other files. In my system, I don't have any solvents, no any waters and no any ion. 
>
> I take the "DRGCNS.TOP  : CNS topology file" and "DRGGMX.ITP  : GROMACS .itp file" and "DRGFIN.GRO  : final coordinates in GROMOS87 format" to gromacs and do "grompp -v", but I get error as below shows:
>
> Fatal error: number of coordinates in coordinate file (drgfin.gro, 15)
>              does not match topology (drgcns.top, 0)
>
> what can I do now? Thank you for you help.
> yafei
>
>
> ----- Original Message -----
> From: Yang Ye <leafyoung at yahoo.com>
> Date: Wednesday, September 5, 2007 2:24 am
> Subject: Re: [gmx-users] pdb file from prodrg2 cannot be recognized by gromacs?
>
>   
>> Hi,
>>
>> You need to get the topology file from PRODRG together with the 
>> PDB file 
>> so you skip pdb2gmx and use the outputs from PRODRG in grompp 
>> directly. 
>> Of cource, do whatever you need to add water and ions before grompp.
>>
>> Regards,
>> Yang Ye
>>
>> On 9/5/2007 10:51 AM, Yafei Dai wrote:
>>     
>>> I got a pdb file from prodrg2 and I did pdb2gmx:
>>>
>>> pdb2gmx -f test.pdb -p test.top -o test.gro
>>>
>>> I was told "DRG" not found in residue topology. What can I do 
>>>       
>> for this error information? My pdb file is as below:
>>     
>>>   
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