Re: [AMBER] Using Antechamber to generate RESP prepi file

From: Lianhu Wei <lianhu.wei.gmail.com>
Date: Wed, 18 Apr 2012 15:27:42 -0400

Dear 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 Wed Apr 18 2012 - 12:30:05 PDT
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