I still don't understand your problem (what are the messages you get from
the program etc...), but if you want send me your resp input files to my
private e-mail (cieplak.cgl.ucsf.edu) and I can test them in my setup.
Piotr
On Thu, 29 Apr 2010, Joćo Henriques wrote:
> From: "[ISO-8859-1] Joćo Henriques" <joao.henriques.32353.gmail.com>
> Sender: amber-bounces.ambermd.org
> To: AMBER Mailing List <amber.ambermd.org>
> Date: Thu, 29 Apr 2010 19:39:39 +0100
> Subject: Re: [AMBER] Fortran runtime error: Bad value during integer read
> Reply-To: AMBER Mailing List <amber.ambermd.org>
>
> For some reason 150.000 points is just too much. It works fine with
> 70.000 (discovered that today). But I really need the maximum number
> of layers possible, so I'll have to take some measures to make Resp
> able to handle 150.000 points. Changing those parameters and
> recompiling is my next objective. I'll ask for some aid with this task
> since my programming is rusty to say the least.
>
> Thanks for the feedback.
>
> Joćo
>
> On Thu, Apr 29, 2010 at 6:56 PM, Piotr Cieplak <cieplak.cgl.ucsf.edu> wrote:
>>
>> I am not sure if I understand what (exactly) is the problem with RESP.
>> This program should accept any number of esp points. It reads the esp
>> points and immediately uses them to create appropriate matrices for charge
>> fitting. The size of those matrices is roughly
>> (nomolecules*natom+lagrangeconstr+1),
>> so - any number of atoms should be handled easily even on the laptops.
>> As I understand RESP in standard version handles 500 atoms, 100 lagrange
>> constraints and 30 molecules. If it nos enough then change maxq, maxlgr and
>> maxmol parameters and recompile.
>>
>> Piotr
>>
>>
>> On Thu, 29 Apr 2010, Joćo Henriques wrote:
>>
>>> From: "[ISO-8859-1] Joćo Henriques" <joao.henriques.32353.gmail.com>
>>> Sender: amber-bounces.ambermd.org
>>> To: AMBER Mailing List <amber.ambermd.org>
>>> Date: Thu, 29 Apr 2010 14:19:13 +0100
>>> Subject: Re: [AMBER] Fortran runtime error: Bad value during integer read
>>> Reply-To: AMBER Mailing List <amber.ambermd.org>
>>>
>>> Ok, as I suspected Resp can't handle such huge ESP files. With 6/42=8
>>> and MK pop the number of points reduces from over 150.000 to aprox.
>>> 70.000 and Resp is finally able to handle them.
>>> I'm kinda surprised no one has ever experienced similar problems. I'll
>>> have to change the source code to make it able to handle bigger files.
>>> If anyone has any ideas about how to change the code, please feel free
>>> to mail me. All ideas are welcome.
>>>
>>> 2010/4/29 Joćo Henriques <joao.henriques.32353.gmail.com>:
>>>>
>>>> I'm 100% sure Resp within AmberTools can handle multi-conformational
>>>> fits. I've done quite a few myself. But I don't know how limited it
>>>> is. I'll run a few tests with less points per each atomic center to
>>>> see if it is due to the cheer size and complexity of my models. I
>>>> provide over 150.000 points for each model (they are 4). So it might
>>>> be too much to handle.
>>>> As a final measure I'll have a serious look at RED. In good truth I
>>>> haven't looked at it more seriously because from what I've read it
>>>> uses AmberTools Resp code. If I can use the code directly why use it
>>>> through an intermediate program. (This consideration might be wrong,
>>>> as I said I haven't done any significant research on RED).
>>>>
>>>> If the limitation in Amber's Resp program is proven this becomes
>>>> serious, since it might occur to other users. Some kind of measure
>>>> should be taken. At least inform users about this limitation.
>>>>
>>>> Thanks for all the feedback, I'm always looking forward to receiving
>>>> more input from experienced users.
>>>>
>>>> On Thu, Apr 29, 2010 at 1:10 PM, Jason Swails <jason.swails.gmail.com>
>>>> wrote:
>>>>>
>>>>> Hello,
>>>>>
>>>>> I'm not sure if RESP included with amber can handle multi-conformational
>>>>> resp fits. I remember reading somewhere that it doesn't, but you said
>>>>> that
>>>>> it did for small molecules, so I'm not quite sure.
>>>>>
>>>>> If you're looking to do some heavy-duty multi-conformational RESP
>>>>> fitting, I
>>>>> would suggest looking at R.E.D., which is linked to from
>>>>> http://ambermd.org. There has been plenty of discussion about it on
>>>>> the Amber list, and it
>>>>> has more capabilities built in than the resp.f included with amber.
>>>>>
>>>>> Good luck!
>>>>> Jason
>>>>>
>>>>> 2010/4/29 Joćo Henriques <joao.henriques.32353.gmail.com>
>>>>>
>>>>>> They were all GNU. GCC and GFORTRAN. A friend researcher of mine used
>>>>>> PGI with 1.4 version of AmberTools and obtained the same error.
>>>>>>
>>>>>> On Thu, Apr 29, 2010 at 2:33 AM, Mengjuei Hsieh <mjhsieh.gmail.com>
>>>>>> wrote:
>>>>>>>
>>>>>>> 2010/4/28 Joćo Henriques <joao.henriques.32353.gmail.com>:
>>>>>>>>
>>>>>>>> It's really confusing. This leads me to suspect that
>>>>>>>> the file size is prohibitive, but if that's the case why isn't there
>>>>>>>> anything written about this on the manual or something. Since I have
>>>>>>>> 99 atoms and I'm calculating the esp with B3LYP/Gen (6-31G(d) and
>>>>>>>> LANL2TZ(f)) with SCF=Tight, Pop(MK,ReadRadii,Full) and
>>>>>>>> IOp(6/33=2,6/41=10,6/42=17) I might have too much points too compute
>>>>>>>> with resp... But again I'm just guessing!
>>>>>>>
>>>>>>> Hi, it is indeed intriguing, what compilers are you using for
>>>>>>> AmberTools? Knowing the kind of compilers might help developers
>>>>>>> tracking down the issues.
>>>>>>>
>>>>>>> Best,
>>>>>>> --
>>>>>>> Mengjuei
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
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>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
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>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Jason M. Swails
>>>>> Quantum Theory Project,
>>>>> University of Florida
>>>>> Ph.D. Graduate Student
>>>>> 352-392-4032
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
>>>
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Received on Thu Apr 29 2010 - 14:00:03 PDT
