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/ADF1ADFf2IY3YV7ADFr8OYbP0kodeOQpVkttuADFADFADF/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 - 03:30:04 PDT
