[gmx-users] Re: Bug? in version 3.1.4

[istvan at kolossvary.hu]

Many thanks, I breathe easier. 

Cheers, 

  Istvan 


Erik Lindahl wrote: 

> Hi Istvan, 
> 
> You're perfectly correct. The problem is that the atom is sometimes called 
> CA and sometimes CH3 in pdb files, but we're working on a more general 
> converter that can accept alternative names for atoms :-) 
> 
> Cheers, 
> 
> Erik 
> 
> On Tuesday, September 23, 2003, at 07:44 AM, istvan at kolossvary.hu wrote: 
> 
>> Hi,
>> I was trying to "pdb2gmx" a simple peptide capped with ACE at the 
>> N-terminus and NAC at the C-terminus, but generating the hydrogens failed 
>> on NAC with an error message coming from genhydro.c "Atom CA not found in 
>> residue NAC3 for while adding hydrogens". It turns out that the problem 
>> is a mismatch between respective .rtp and .hdb files. I specifically 
>> worked with oplsaa, but it seems that similar mismatches are present in 
>> the other force field files, too. For example, for oplsaa, the NAC carbon 
>> is a CH3 in the .rtp file, which is correct, but the same carbon in the 
>> corresponding .hdb file is a CA, which seems incorrect, because NAC does 
>> not have a CA. Changing the CA to CH3 in the .hdb file solved the 
>> problem. Since I am new to Gromacs, I am not sure that this is a correct 
>> fix, or I am missing something.
>> Thanks for your help.
>>  Istvan Kolossvary _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the www 
>> interface or send it to gmx-users-request at gromacs.org.
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.