Dear Francois,
I used two machine, I got two different results. I am going to report this bug.
Thanks,
William
On 4/19/12, FyD <fyd.q4md-forcefieldtools.org> wrote:
> William,
>
> - I think you need to generate two resp inputs for the two RESP stages;
> See for instance (but he atom order is different to yours)
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFf2IY3YV7ADFr8OYbP0kodeOQpVkttuADFADFADF/P7688/Data-R.E.D.Server/input1_m1
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFf2IY3YVFrancois7ADFr8OYbP0kodeOQpVkttuADFADFADF/P7688/Data-R.E.D.Server/input2_m1
>
> - then, I would carefully check how "respgen" works in the AmberTools
> manual...
>
> regards, Francois
>
>
>> Thank you very much for your kindly help. the commands I used to
>> generate these files are:
>>
>> $antechamber -fi gout -i KP92_Esp_Low.log -fo prepi -o KP92_Low.prepi
>> -c resp -j 4 -at amber -rn KP92
>>
>> $antechamber -fi gout -fo ac -i KP92_Esp_Low.log -o KP92_Low_RESP.ac -c
>> resp
>>
>> $antechamber -fi ac -i KP92_Low_RESP.ac -c wc -cf KP92_Low_RESP.crg
>>
>> The charge looks not right, So I used espgen and respgen:
>>
>> $espgen -i KP92_Esp_Low.log -o KP92_Esp_Low_espgen.esp
>>
>> $respgen -i KP92_Low_RESP.ac -o KP92_Esp_Low_respgen.respin -f resp
>>
>> The charge generated are same.
>>
>> I attached the files these commands generated. Please let me know if
>> you need more information to diagnose this problem. This Molecule
>> should have +1 charge.
>>
>> Thanks,
>> William
>>
>> On 4/18/12, FyD <fyd.q4md-forcefieldtools.org> wrote:
>>> William,
>>>
>>>> Yes, I want to derive RESP charges and force field for the whole
>>>> molecule.
>>>
>>> ok, so the RESP inputs should be easy to generate...
>>>
>>>> So I followed the manu of antechamber. What I found is the
>>>> charges are weird big.
>>>
>>> Yes, for sure there is something wrong...
>>>
>>>> I do not know the reason. I am wondering if I
>>>> used wrong setting for Gaussian or I misused antechamber. I hope
>>>> somebody can give me some clue for this issue.
>>>
>>> Your MEP file seems OK to me - although IOp(6/33=2,6/41=4,6/42=4) do
>>> not correspond to the default in Gaussian.
>>>
>>> Could you send us the 2 RESP inputs you generated, as well as all the
>>> commands you used to derive these charge values?
>>>
>>> regards, Francois
>>>
>>>
>>>> On 4/18/12, FyD <fyd.q4md-forcefieldtools.org> wrote:
>>>>> Dear William,
>>>>>
>>>>> This is difficult to help as you did not provide a lot information
>>>>> about what you did...
>>>>>
>>>>> I looked at your structure and it looks like a modified amino-acid,
>>>>> but not exactly as this is not a dipeptide... Do you want to derive
>>>>> RESP charges for this whole molecule? or do you want to derive charges
>>>>> for a particular/corresponding fragment? (one could understand errors
>>>>> (i. e. the bad charge values you reported) in the fit if the
>>>>> constraints defined to design the fragments are not well defined...).
>>>>>
>>>>> I used R.E.D. Server as defined at:
>>>>> http://q4md-forcefieldtools.org/REDS/faq.php#3 &
>>>>> http://q4md-forcefieldtools.org/REDS/faq.php#21
>>>>>
>>>>> - The Ante_R.E.D. 2.0 job to generate the .P2N file: R.E.D. Server job:
>>>>> P7686
>>>>> (the atom order has been modofied by Ante_R.E.D.
>>>>> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFCFjrwFXVADFHRGSLxADFtyG6W2JoWTysLt1/P7686.html
>>>>> The corresponding Java applet:
>>>>> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFCFjrwFXVADFHRGSLxADFtyG6W2JoWTysLt1/P7686/javaappletp2n-1.html
>>>>> The corresponding P2N file:
>>>>> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFCFjrwFXVADFHRGSLxADFtyG6W2JoWTysLt1/P7686/Mol_antered1-out.p2n
>>>>>
>>>>> - Then, I modified the total charge value of your molecule in the P2N
>>>>> file
>>>>> REMARK CHARGE-VALUE 1
>>>>>
>>>>> - The R.E.D. IV job to generate the .mol2 file: R.E.D. Server job:
>>>>> P7688
>>>>> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFf2IY3YV7ADFr8OYbP0kodeOQpVkttuADFADFADF/P7688.html
>>>>> The corresponding Java applet:
>>>>> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFf2IY3YV7ADFr8OYbP0kodeOQpVkttuADFADFADF/P7688/javaappletmol2-1.html
>>>>> The corresponding mol2 file:
>>>>> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFf2IY3YV7ADFr8OYbP0kodeOQpVkttuADFADFADF/P7688/Data-R.E.D.Server/Mol_m1-o1.mol2
>>>>>
>>>>> -> the optimized geometry is similar to that you reported in the
>>>>> "KP92_Esp_Low.log" MEP file...
>>>>> (you have an intra-molecular hydrogen bond that might not be
>>>>> suitable...)
>>>>>
>>>>> -> As you can see in the .mol2 file (a FF library file format similar
>>>>> to the prep one; See
>>>>> http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php &
>>>>> http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php) all the charge
>>>>> values seems reasonable...
>>>>>
>>>>> I hope this helps...
>>>>>
>>>>> regards, Francois
>>>>>
>>>>> PS By now, any user can follow the R.E.D. Server .log file (provides
>>>>> the status of the job) from the Qstat interface...
>>>>> See http://cluster.q4md-forcefieldtools.org/qstat/
>>>>>
>>>>>
>>>>>> I am using Gaussian 09 version c.01 to perfrom optimization and esp
>>>>>> density calculation. When I used Antechamber to generate prepi file
>>>>>> using RESP charge, I fond many atom have charge larger than 1 or
>>>>>> smaller than -1. Here is my gaussian input:
>>>>>> ====
>>>>>> %chk=./KP92_ESP_Low.chk
>>>>>> #HF/6-31G* SCF=Tight Pop=MK Geom=AllCheck Guess=Read
>>>>>> IOp(6/33=2,6/41=4,6/42=4)
>>>>>>
>>>>>> KP92 ESP charge high density
>>>>>>
>>>>>> 1 1
>>>>>> ==========
>>>>>>
>>>>>> I am using the following command to generate prepi file:
>>>>>> antechamber -fi gout -i KP92_Esp_Low.log -fo prepi -o KP92_Low.prepi
>>>>>> -c resp -j 4 -at amber -rn KP92
>>>>>>
>>>>>> Here is the file I generated:
>>>>>> =========
>>>>>>
>>>>>> $ more KP92_Low.prepi
>>>>>> 0 0 2
>>>>>>
>>>>>> This is a remark line
>>>>>> molecule.res
>>>>>> KP92 INT 0
>>>>>> CORRECT OMIT DU BEG
>>>>>> 0.0000
>>>>>> 1 DUMM DU M 0 -1 -2 0.000 .0 .0
>>>>>> .00000
>>>>>> 2 DUMM DU M 1 0 -1 1.449 .0 .0
>>>>>> .00000
>>>>>> 3 DUMM DU M 2 1 0 1.522 111.1 .0
>>>>>> .00000
>>>>>> 4 O3 O M 3 2 1 1.540 111.208 180.000
>>>>>> -1.501803
>>>>>> 5 C7 C M 4 3 2 1.226 68.464 -43.436
>>>>>> 2.155189
>>>>>> 6 C8 CT 3 5 4 3 1.513 123.380 -31.018
>>>>>> 4.993839
>>>>>> 7 H11 HC E 6 5 4 1.094 113.517 -172.179
>>>>>> -1.612854
>>>>>> 8 H12 HC E 6 5 4 1.096 108.824 66.261
>>>>>> -1.612854
>>>>>> 9 H13 HC E 6 5 4 1.093 108.913 -50.338
>>>>>> -1.612854
>>>>>> 10 N3 N M 5 4 3 1.380 120.343 149.629
>>>>>> -4.227657
>>>>>> 11 H10 H E 10 5 4 1.011 119.713 -165.969
>>>>>> 1.203058
>>>>>> 12 C2 CT M 10 5 4 1.452 117.929 -8.719
>>>>>> 4.340736
>>>>>> 13 C1 C B 12 10 5 1.526 111.997 -159.390
>>>>>> -0.741272
>>>>>> 14 O1 O E 13 12 10 1.225 123.452 -151.271
>>>>>> 0.037839
>>>>>> 15 O2 OS S 13 12 10 1.325 113.176 30.494
>>>>>> -0.797118
>>>>>> 16 C9 CT 3 15 13 12 1.453 117.159 177.504
>>>>>> 4.006875
>>>>>> 17 H14 H1 E 16 15 13 1.091 109.842 60.796
>>>>>> -1.213156
>>>>>> 18 H15 H1 E 16 15 13 1.092 109.709 -60.215
>>>>>> -1.213156
>>>>>> 19 H16 H1 E 16 15 13 1.088 105.038 -179.632
>>>>>> -1.213156
>>>>>> 20 H1 H1 E 12 10 5 1.104 107.621 -42.807
>>>>>> -1.164949
>>>>>> 21 C3 CT M 12 10 5 1.547 112.374 75.545
>>>>>> 1.281904
>>>>>> 22 H2 HC E 21 12 10 1.094 109.757 85.172
>>>>>> -0.802035
>>>>>> 23 H3 HC E 21 12 10 1.091 107.929 -32.252
>>>>>> -0.802035
>>>>>> 24 C4 CT M 21 12 10 1.541 110.869 -151.779
>>>>>> 4.097580
>>>>>> 25 H4 H1 E 24 21 12 1.091 110.308 83.816
>>>>>> -1.272201
>>>>>> 26 H5 H1 E 24 21 12 1.095 111.537 -35.165
>>>>>> -1.272201
>>>>>> 27 N1 NT M 24 21 12 1.474 113.240 -156.118
>>>>>> -2.261363
>>>>>> 28 H6 H E 27 24 21 1.013 117.985 -99.702
>>>>>> 0.245473
>>>>>> 29 C5 CM M 27 24 21 1.325 124.425 79.906
>>>>>> 1.707264
>>>>>> 30 N2 NT B 29 27 24 1.316 122.276 -2.405
>>>>>> -2.342325
>>>>>> 31 H9 H E 30 29 27 1.015 118.201 -179.452
>>>>>> 0.807641
>>>>>> 32 H17 H E 30 29 27 1.032 123.585 -6.081
>>>>>> 0.807641
>>>>>> 33 C6 CT M 29 27 24 1.519 116.883 174.249
>>>>>> 3.546339
>>>>>> 34 H7 H1 E 33 29 27 1.093 109.683 41.607
>>>>>> -1.007917
>>>>>> 35 H8 H1 E 33 29 27 1.093 108.694 -77.245
>>>>>> -1.007917
>>>>>> 36 Cl1 Cl M 33 29 27 1.788 113.745 162.660
>>>>>> -1.552555
>>>>>>
>>>>>>
>>>>>> LOOP
>>>>>>
>>>>>> IMPROPER
>>>>>> C8 N3 C7 O3
>>>>>> C7 C2 N3 H10
>>>>>> C2 O1 C1 O2
>>>>>> C6 N1 C5 N2
>>>>>>
>>>>>> DONE
>>>>>> STOP
>>>>>> =========
>>>>>>
>>>>>> I attached my gaussian log file. Could anybody help me with this big
>>>>>> number of RESP charge issue?
>
>
>
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Received on Thu Apr 19 2012 - 09:00:04 PDT
