[gmx-users] Re: question about gromacs (4.5) installation

Moeed lecielll at googlemail.com
Thu Mar 10 20:57:33 CET 2011


Hello,

If you need to keep ions.top then see the below link:

http://lists.gromacs.org/pipermail/gmx-users/2010-September/054487.html

moeed

On 10 March 2011 14:53, tao wei <twei2004 at gmail.com> wrote:

> Dear Moeed,
>
> Thanks a lot for your quick response!
> That is problem. I do need to include ions.itp.
>
> Is there anything wrong on this file? Does Gromacs mis-understand C* with
> CU2+ ?
> Do you think if i only keep the necessary line for these ions that i need?
> Thanks for your suggestions!
>
> Now temporally grompp with the old version of Gromacs, and put it to run it
> on the cluster
> with new version. But I should find out what is going on for this new
> version.
>
> tao
>
>
> On Thu, Mar 10, 2011 at 1:49 PM, Moeed <lecielll at googlemail.com> wrote:
>
>> Hi,
>>
>> Please don't #include "ions.itp" in your topology file if not needed.
>>
>> moeed
>>
>>
>> On 10 March 2011 13:22, tao wei <twei2004 at gmail.com> wrote:
>>
>>> Hi
>>>
>>> I saw your post on Gromacs forum about the
>>>
>>> Fatal error:
>>> Atomtype CU2+ not found
>>>
>>> http://lists.gromacs.org/pipermail/gmx-users/2010-September/053804.html
>>>
>>>
>>>
>>> I have found that i have the same problem.
>>> I grompp my file with gromacs-4.0.5. I have no problem.
>>> But if I change to gromacs-4.5.3
>>> Gromacs just gave me this error report, like yours
>>> It looks very strange.
>>>
>>>
>>>
>>> Have you solved the problem?
>>> Thanks for your information!
>>>
>>> tao
>>>
>>>
>>
>
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