Dear Francois,
Yes, I want to derive RESP charges and force field for the whole
molecule. So I followed the manu of antechamber. What I found is the
charges are weird big. 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.
I will try to follow RED later.
Thanks,
William
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 Wed Apr 18 2012 - 07:00:02 PDT
